Empirical evidence indicates that for two reef fish groups, chaetodontids and pomacanthids, live coral cover and latitude determine the local abundance and species richness patterns. Most studies have considered the influence of either live coral cover or latitude in isolation, and the interactive effects that are likely to influence the geographical distribution in species richness and diversity has not been explored. In this study we explored the relationship between (1) species richness and latitude, and (2) species richness and benthic variables, (3) species diversity and latitude and (4) species diversity and benthic variables for butterflyfish (Chaetodontidae) and angelfish (Pomacanthidae) at 75 sites across 51 islands in the Andaman and Nicobar (A & N) archipelago. A total of 30 species of chaetodontids belonging to four genera and 13 species of pomacanthids belonging to nine genera were recorded. We found that live coral cover and latitude were the best predictors for explaining variation in the distribution of these fish communities across the A & N archipelago. This is probably because of the high dependence of these two fish groups on live coral cover and Nicobar’s geographical proximity to the Coral Triangle, which is considered to be the center of origin of coral reefs and supports high biodiversity. Our results show that despite the high dependence of chaetodontids and pomacanthids on live coral cover, reduction of live coral cover due to a series of disturbance events had limited influence on species richness of these two fish groups, indicating that broad geographical trends are important in explaining variation in species richness for chaetodontid and pomacanthid fish groups.