We investigated the effect of interannual variation on the biodiversity and distribution of decapod larvae at Saint Paul's Rocks, an isolated small group of equatorial islands linked to the Atlantic Mid-Ocean ridge. Zooplankton samples were collected between 2003 and 2005 from a range of different environments off the archipelago. Horizontal surface hauls were conducted in the inlet and at three increasing distances from the archipelago, both in the morning and at night, using a 200-μm mesh net. Decapod larvae collected included 11 species and 37 individual taxa. Seven of them have not previously been recorded in the area. Samples taken at the shortest distance from the archipelago exhibited a significantly greater abundance than samples taken further away. No significant differences were detected between months in terms of decapod larvae abundance in the inlet. However, in the open ocean at night, the mean abundance was much higher in May and July. Decapod larvae abundance was much higher at night for both the open ocean and the inlet. Brachyuran and caridean larvae exhibited the greatest abundance and frequency in the inlet, mainly represented by the first-stage larvae of: Grapsus grapsus, Plagusia depressa, Platypodiella spectabilis and Alpheidae. In contrast, Sergestidae holopelagic shrimps were the most abundant and the most frequent larvae in the surface waters of the open ocean. The composition, abundance and distribution of decapod larvae were very similar during the 2 years sampled. Species accumulation curves indicate that even greater diversity exists, demonstrating that long-term research is important for acquiring accurate knowledge about the biodiversity of dynamic ecosystems such as those at Saint Paul's Rocks.