The photographs reflect the contents of the whole collection and relate to marine ecology and fauna; natural history; anthropology and personal subjects.
- Personal subjects, some 200 - 250 b/w and sepia images of Thompson and various family members ca. 1860-ca. 1950. These include: Personal subjects, some 200 - 250 b/w and sepia images of Thompson and various family members ca. 1860-ca. 1950. These include: Portrait images of Gamgee family members (Edinburgh Veterinary pioneers, ca. 1860-ca. 1875); Portrait images of Gamgee family members (Edinburgh Veterinary pioneers, ca. 1860-ca. 1875); Irish family members- Thompson being the son of Thompson the elder's first marriage, he subsequently re-married after moving to Galway and had a large family). This family took the surname Thompson (images date from ca. 1885-ca. 1935); Irish family members- Thompson being the son of Thompson the elder's first marriage, he subsequently re-married after moving to Galway and had a large family). This family took the surname Thompson (images date from ca. 1885-ca. 1935); Portrait photographs of Thompson (ca. 1885-ca. 1947); Portrait photographs of Thompson (ca. 1885-ca. 1947); Thompson, wife and children images (ca. 1905-ca. 1950); Thompson, wife and children images (ca. 1905-ca. 1950); Photographs of Thompson on various of his travels including the United States (1936) and Greece (1939).
- International Fur Seal Commission: some 250 -300 b/w and sepia images up to 60x20cm of the Pribiloff Islands, Behring Sea, 1894 - 1897. The images include photographs taken during these expeditions by Alexander (Alec) Masterman Rodger, one of Thompson's assistants at UCD who later became Curator of Perth City Museum (Scotland). The stock of images also include a quantity of photographs dated 1894. The provenance of these holdings can be assumed but is not known.
- Location shots: some 20 - 30 b/w images not including Thompson. Prominent amongst these is an image of Thompson's study at UCD (ca. 1900) and exterior and interior images of his homes of Gowrie Cottage, Broughty Ferry (Angus) where he lived from ca.1884-1917, and 44 South Street, St Andrews (1917-1948).
- Lantern slides: some 250 slides, many of which have been digitised: fisheries research - Scotland-based (ca. 1900-ca.1935); Aran Islands (Ireland) life and views (ca. 1930-1935).
- University of St Andrews Natural History teaching lantern slides: some 300 in total.
- Scientific photographs showing structure in nature: Some 30-50 images relating to On Growth and Form, ca. 1915-ca. 1940. These were obtained by Thompson from various sources and include a noted early water splash image.