Abstract The coral reefs around Praia do Tofo and Praia da Barra, southern Mozambique, are known for their aggregations of marine megafauna but few studies have examined their reef fish biodiversity. This study assesses for the first time the ichthyofaunal diversity of the seas around Praia do Tofo and Praia da Barra. Methods involved underwater observations during recreational dives between February and September 2016, and the use of photographic records from 2015. A total of 353 species, representing 79 families, were recorded from 16 patch reefs in the region. The area shows comparable species diversity to others in the southwestern Indian Ocean, suggesting these reefs are in good condition. But high primary productivity driven by coastal upwelling may make fish diversity and trophic structure unreliable measures of the health of these reefs. Future studies investigating the sustainability of this ecosystem would benefit from utilising a wide range of reef health measures.