The temporal structure of reef fish post-larvae assemblages were examined at two sites on the southwest coast of Madagascar: Nosy Ve Island, off Anakao, where every forms of fishing have been banned since 1999, and the north of the Great Barrier Reef of Toliara which has been impacted by overfishing for years. Fish post-larvae were collected using light traps during five nights of the new moon periods from August 2013 to February 2014. A total of 34 and 36 families grouping 95 and 101 different morphospecies were collected from the two sites respectively. At both sites, fish post-larvae were more abundant and diverse from December to January. Significant differences in the assemblage structure of reef fish post-larvae were detected between seasons due to the Pomacentridae (Pomachromis richardsoni and Parma spp1), Mullidae (Parupeneus spp), Siganidae (Siganus sutor) and Blenniidae (Istiblennius edentulus). The relationship between fish post-larval assemblage and abiotic factors differed between the two sites. At the Anakao site, temperature and water transparency explained 26.4% of the variability observed in fish post-larvae assemblages when at the Great Barrier Reef site, these two variables and salinity explained 20.7% only. All these results are discussed in the context of the development of post-larvae capture and culture for ornamental fish market and food fish rearing.