| RefNo | Title | Date |
| NLB/13/363 | Copy letter from Theodore E James, to Messrs Harrison & Sons | 1 August 1896 |
| EC/1859/08 | Macdonald, Sir John Denis: certificate of election to the Royal Society | |
| AP/34/16/3 | Unpublished figures, magnified crustacean antennae by John Denis MacDonald | December 1852 |
| NLB/4/702 | Copy letter from Herbert Rix, to Dr John Denis Macdonald, Fellow of the Royal Society | 1 October 1890 |
| NLB/3/489 | Copy letter from Herbert Rix, to Dr John Denis Macdonald, Fellow of the Royal Society | 22 June 1889 |
| NLB/3/488 | Copy letter from Herbert Rix, to Professor Michael Foster, [Secretary, Royal Society] | 22 June 1889 |
| NLB/3/994 | Copy letter from Herbert Rix, to Dr John Denis Macdonald, La Maisonette, Claremonth Road, Surbiton | 3 December 1889 |
| NLB/3/948 | Copy letter from [John William Strutt] Lord Rayleigh, to Dr John Denis Macdonald, Fellow of the Royal Society | 21 November 1889 |
| NLB/11/664 | Copy letter from Theodore E James, to Dr John Denis Macdonald, Fellow of the Royal Society | 6 September 1895 |
| NLB/19/625 | Copy letter from Theodore E James, to Dr John Denis Macdonald, Fellow of the Royal Society | 11 November 1899 |
| AP/39/39/8 | Unpublished figure, 'Inferior palial [pallial] artery' by John Denis Macdonald | March 1857 |
| NLB/10/252 | Copy letter from Theodore E James, to Messrs Harrison & Sons | 1 November 1894 |
| AP/39/39/3 | Unpublished figure, 'Contractile portion of the bulbous arteriosus' by John Denis Macdonald | March 1857 |
| NLB/19/705 | Copy letter from Robert William Frederick Harrison, to Dr John Denis Macdonald, Fellow of the Royal Society, Chairminster House, Dorchester, Dorset | 27 November 1899 |
| NLB/36/418 | Copy letter from Robert William Frederick Harrison, to Sir John Denis Macdonald, Fellow of the Royal Society | 28 October 1907 |
| NLB/37/192 | Copy letter from Robert William Frederick Harrison to Harrison & Sons | 12 February 1908 |
| PT/51/5/2 | Plate, figures 1-4 showing several views of the Macgillivrayia pelagica by J D M [John Denis Macdonald] | 11 February 1854 |
| MC/12/154 | Letter from John D [Denis] Macdonald, [?] Netley, Southampton, to [Thomas Henry] Huxley, [Secretary of the Royal Society] | 12 March 1881 |
| PT/51/4/2 | Plate, 'Left lateral view of N. umbilicatus removed from the shell' by J D [John Denis] Macdonald | [1854] |
| RR/7/311 | Referee's report by John Denis Macdonald, on a paper 'Contributions to the development history of the mollusca' by Edwin Ray Lankester | 1 April 1874 |
| AP/69/7 | Unpublished paper, 'Analogy of sound and colour; comparison of the seven colours of the rainbow with the seven notes of the musical scale as determined by the monochord, and of the wavelengths of colour and sound' by John [Denis] Macdonald | 1893 |
| AP/69/7/3 | Unpublished letter, regarding 'Outline of the practical application of musical harmony to colours' from John Denis Macdonald to Herbert Rix | 24 March 1893 |
| AP/69/7/2 | Unpublished diagrams, 'Outline of the practical application of musical harmony to colours' by John Denis Macdonald | 1893 |
| AP/39/39/7 | Unpublished figures, pallial recurrent arteries by John Denis Macdonald | March 1857 |
| AP/69/7/1 | Unpublished manuscript, 'Analogy of sound and colour; comparison of the seven colours of the rainbow with the seven notes of the musical scale as determined by the monochord, and of the wavelengths of colour and sound' by John [Denis] Macdonald | 1893 |
| RR/4/158 | Referee's report by George Busk, on three unnamed papers by John Denis MacDonald | 4 February 1859 |
| RR/2/142 | Referee's report by George Newport, on a paper 'On the anatomy of Nautilus umbilicatus, compared with that of Nautilus pompilius' by John Denis MacDonald | 26 May 1853 |
| PT/51/4/1 | Manuscript, 'On the anatomy of Nautilus umbilicatus compared with that of Nautilus pompilius' by John Denis Macdonald | [1854] |
| PT/51/4 | Paper, 'On the anatomy of Nautilus umbilicatus compared with that of Nautilus pompilius' by John Denis Macdonald | [1854] |
| PT/51/6/1 | Manuscript, 'Further observations on the anatomy of Macgillivrayia, Cheletropis, and allied genera of pelagic gasteropoda' by John Denis Macdonald | [1855] |
| PT/51/6/2 | Plate, figures 16-24 showing the Macgillivrayia pelagica and other pelagic gasteropods by J D [John Denis] Macdonald | 11 February 1854 |
| RR/2/140 | Referee's report by Thomas Henry Huxley, on a paper 'Further observations on the anatomy of Macgillivrayia, Cheletropis, and allied genera of pelagic gasteropoda' by John Denis MacDonald | nd [1855] |
| PT/51/4/4 | Plate, figures 3-8 showing parts of the auditory and lingual anatomy of the nautilus by J D [John Denis] Macdonald | [1854] |
| PT/51/5/3 | Plate, figures 5-15 showing parts of the anatomy of the Macgillivrayia pelagica and the Cheletropis huxleyi by J D M [John Denis Macdonald] | 11 February 1854 |
| PT/51/4/5 | Plate, figures 9-16 showing renal and epithelial parts of the anatomy of the nautilus by J D [John Denis] Macdonald | [1854] |
| PT/51/4/3 | Plate, 'Simple dissection of the nautilus' by J D [John Denis] Macdonald | [1854] |
| MC/7/216 | Letter from John D [Denis] Macdonald, Haslar Hospital, Gosport, Hampshire, to Dr [William] Sharpey, Secretary of the Royal Society | May 1865 |
| MC/7/217 | Letter from John D [Denis] Macdonald, Haslar Hospital, Gosport, Hampshire, to Dr [William] Sharpey, Secretary of the Royal Society | 27 May 1865 |
| MC/7 | Volume 7 of miscellaneous correspondence regarding business matters, sent to the Royal Society | 1864-1866 |
| PT/51/5 | Paper, 'Remarks on the anatomy of Macgillivrayia pelagica, and Cheletropis huxleyi (Forbes). Suggesting the establishment of a new order of gasteropoda' by John D [Denis] Macdonald | 11 February 1854 |
| MC/10/136 | Letter from John Denis Macdonald, Weston Grove Road, Woolston, Southampton, to Walter White, Assistant Secretary of the Royal Society, Burlington House | 29 June 1874 |
| MC/10 | Volume 10 of miscellaneous correspondence regarding business matters, sent to the Royal Society | July 1873-1876 |
| PT/51/5/1 | Manuscript, 'Remarks on the anatomy of Macgillivrayia pelagica, and Cheletropis huxleyi (Forbes). Suggesting the establishment of a new order of gasteropoda' by John D [Denis] Macdonald | 11 February 1854 |
| AP/39/14 | Paper, 'Brief description of a ctenostomatous polyzoon, allied to Vesicularia, cccurring on the Australian coast' by John Denis Macdonald | April 1856 |
| RR/2/143 | Referee's report by William Spence, on a paper 'On the anatomy of Nautilus umbilicatus, compared with that of Nautilus pompilius' by John Denis MacDonald | 30 May 1853 |
| AP/34/16/2 | Unpublished figures, crustacean antennae by John Denis MacDonald | December 1852 |
| AP/34/16 | Unpublished paper, 'Observations on the anatomy of the antennae in a small species of crustacean' by John Denis MacDonald | December 1852 |
| RR/2/141 | Referee's report by Thomas Bell, on a paper 'Further observations on the anatomy of Macgillivrayia, Cheletropis, and allied genera of pelagic gasteropoda' by John Denis MacDonald | nd [1855] |
| AP/37/6/3 | Unpublished figures, Phyllirrhoe bucephala muscular fibres and ovary membrane by John Denis MacDonald | 1854 |
| AP/37/6/4 | Unpublished figures, Phyllirrhoe bucephala brain by John Denis MacDonald | 1854 |
| AP/37/7/2 | Unpublished figures, anatomy of Jasonilla by John Denis MacDonald | 1854 |
| RR/3/191 | Referee's report by Thomas Henry Huxley, on two papers, 'Observations on the anatomy and affinities of the Phyllirrhoë bucephala' and 'Brief sketch of the anatomy of a new genus of pelagic gasteropoda, named Jasonilla' by John Denis MacDonald | 1856 |
| AP/37/6/2 | Unpublished figures, Phyllirrhoe bucephala by John Denis MacDonald | 1854 |
| AP/37/7/1 | Unpublished manuscript, 'Brief sketch of the anatomy of a new genus of pelagic Gasteropoda [sic] named Jasonilla' by John Denis MacDonald | 10 December 1854 |
| AP/37/6 | Paper, 'Observations on the anatomy and affinities of Phyllirrhoe bucephala' by John Denis MacDonald | 10 December 1854 |
| AP/37/6/1 | Manuscript, 'Observations on the anatomy and affinities of Phyllirrhoe bucephala' by John Denis MacDonald | 10 December 1854 |
| AP/37/7 | Unpublished paper, 'Brief sketch of the anatomy of a new genus of pelagic Gasteropoda [sic] named Jasonilla' by John Denis MacDonald | 10 December 1854 |
| AP/39/19 | Paper, 'Anatomical description of a species of asteroid polypes, probably forming the type of a new genus of Alcyonidae' by John Denis Macdonald | April 1856 |
| AP/39/16 | Unpublished paper, 'On the sea saw-dust [Trichodesmium] of the Pacific' by John Denis Macdonald | 1856 |
| AP/39/15/3 | Unpublished figures, lingual teeth of marine gastropods by John Denis Macdonald | May 1856 |
| AP/39/14/2 | Unpublished figures, anatomy of a ctenostomatous polyzoon by John Denis Macdonald | April 1856 |
| AP/39/13/2 | Unpublished figure, nautilus anatomy by John Denis Macdonald | April 1856 |
| AP/39/13 | Paper, 'Further observations on the anatomy and physiology of nautilus' by John Denis Macdonald | April 1856 |
| AP/39/13/1 | Manuscript, 'Further observations on the anatomy and physiology of nautilus' by John Denis Macdonald | April 1856 |
| AP/39/16/1 | Unpublished manuscript, 'On the sea saw-dust [Trichodesmium] of the Pacific' by John Denis Macdonald | 1856 |
| AP/39/14/1 | Manuscript, 'Brief description of a ctenostomatous polyzoon, allied to Vesicularia, cccurring on the Australian coast' by John Denis Macdonald | April 1856 |
| AP/39/16/2 | Unpublished figures, 'The "sea saw dust" of the South Pacific' by John Denis Macdonald | 1856 |
| AP/39/15/1 | Manuscript, 'Observations on the natural affinities and classification of Gasteropoda' by John Denis Macdonald | May 1856 |
| AP/39/15 | Paper, 'Observations on the natural affinities and classification of Gasteropoda [Gastropoda]' by John Denis Macdonald | May 1856 |
| MC/12/168 | Letter from John D [Denis] Macdonald, Alexandra Villa, [?], West Cowes, Isle of Wight, to [Thomas Henry] Huxley, [Secretary of the Royal Society] | 6 June 1881 |
| AP/39/19/2 | Unpublished figures, anatomy of asteroid polypes by John Denis Macdonald | April 1856 |
| AP/39/19/1 | Manuscript, 'Anatomical description of a species of asteroid polypes, probably forming the type of a new genus of Alcyonidae' by John Denis Macdonald | April 1856 |
| AP/39/39/5 | Unpublished figure, 'The ventricle' by John Denis Macdonald | March 1857 |
| AP/39/39/4 | Unpublished figure, 'Short tubule connecting the bulb arteriosus with the ventricle' by John Denis Macdonald | March 1857 |
| AP/39/39/9 | Unpublished letter, regarding 'On the anatomy of Tridacna' from John Denis Macdonald to John Liddell | 10 April 1857 |
| AP/39/39/6 | Unpublished figure, 'Pedicle of the ventricle' by John Denis Macdonald | March 1857 |
| AP/39/39/1 | Unpublished manuscript, 'On the anatomy of Tridacna' by John Denis Macdonald | March 1857 |
| MC/12 | Volume 12 of miscellaneous correspondence regarding business matters, sent to the Royal Society | 1880-1883 |
| AP/39/39/2 | Unpublished figure, 'Pericardium' by John Denis Macdonald | March 1857 |
| AP/39/39 | Unpublished paper, 'On the anatomy of Tridacna' by John Denis Macdonald | 1857 |
| AP/34/16/1 | Unpublished manuscript, 'Observations on the anatomy of the antennae in a small species of crustacean' by John Denis MacDonald | December 1852 |
| PP/6/27/1 | Manuscript, 'On the general characters of the genus Cymbulia' by John D [Denis] Macdonald | 20 March 1885 |
| PP/6/27 | Paper, 'On the general characters of the genus Cymbulia' by John D [Denis] Macdonald | 20 March 1885 |
| PP/6/27/2 | Figures, 'Figure of Cymbulia peronii (Indian Ocean) drawn from nature' by John D [Denis] Macdonald | 1885 |
| AP/39/15/2 | Unpublished figures, Anatomy of marine gastropods by John Denis Macdonald | May 1856 |
| PT/51/6 | Paper, 'Further observations on the anatomy of Macgillivrayia, Cheletropis, and allied genera of pelagic gasteropoda' by John Denis Macdonald | [1855] |
| RR/3/192 | Referee's report by Thomas Bell, on two papers, 'Observations on the anatomy and affinities of the Phyllirrhoë bucephala' and 'Brief sketch of the anatomy of a new genus of pelagic gasteropoda, named Jasonilla' by John Denis MacDonald | 1856 |