We studied the impact of dung deposition by the red howler monkey (Alouatta seniculus), and subsequent burial by dung beetles and other biotic and abiotic processes, on the distribution of small seeds in the soil seed bank (Nouragues Reserve, French Guiana). Seeds were collected from 54 soil samples taken under three sleeping sites and adjoining control sites, at three positions according to a fixed grid and at three different depths (0–2, 2–4 and 4–6 cm). Despite large differences between the three sites, defecation areas (latrines) were found to contain more seeds and higher seed diversity than control areas. Seed density decreased with depth in the top 6 cm in two sites but not in the third. Shannon diversity decreased with depth in both defecation and control areas. Differences in the distribution of seeds of different species were found according to size and growth habits (pioneer vs non-pioneer species). The viability of seeds, ascertained from toughness and integrity of the seed coat, varied according to depth, site and defecation. Seed viability was on average higher in defecation areas compared with control areas.