Coral reef micro-invertebrates are a diverse and abundant group of taxa that inhabit the reef framework structure. However, knowledge about their diversity and function is scarce, limiting our understanding of the responses of coral reef ecosystems to degradation as a whole. We investigated the variability of the cryptofauna community structure in a gradient of live coral cover in La Azufrada coral reef in Isla Gorgona, Colombian Pacific. Live coral cover was estimated from photo-quadrats at 60 sampling points across the reef, where the cryptofauna were also collected in dead coral and coral rubble. Using microscopy to identify taxa, we found 197 morphospecies, among which crustaceans (40%), polychaetes (24%), and molluscans (22%) represented most of the species richness. The 0-25%, 25%-50%, and 50-75% cover categories of live coral were similar to one another in cryptofauna species richness and abundance, but cryptofauna abundance was significantly lower in the areas of highest coral cover (75-100%). Crustaceans were the most abundant group at all four cover categories, mainly due to high abundances of tanaidaceans and isopods. Polychaetes were more abundant in the areas of low coral cover (<25%), whereas echinoderms, represented mostly by ophiuroids, had highest abundances at intermediate levels of coral cover (25%-75%). In contrast to abundance, echinoderms and polychaetes were the major contributors to cryptofauna biomass, whereas the contribution of crustaceans was relatively lower. Our results agree with previous studies in the Eastern Tropical Pacific that have found higher species richness and abundance of cryptic invertebrates in areas with low and intermediate levels of live coral cover. Therefore, substrate heterogeneity is an important condition for the high biodiversity observed in coral reefs.