Astaxanthin is a high value xanthophyll carotenoid with applications in the fields of nutrition and health in particular, due to its antioxidant properties among other bioactivities. Although synthetic astaxanthin is currently dominant in the global market, consumers increasingly prefer astaxanthin from natural sources for human applications. In this context, the production of natural astaxanthin could represent a great economic opportunity for insular territories such as Reunion Island to develop local alternatives to the importation of goods. The aim of this study was to search within the freshwater biodiversity of Reunion Island for strains of microalgae capable of producing and accumulating astaxanthin. During this study, 11 strains were isolated from freshwater samples collected throughout the island. These strains showed similar morphological characteristics with Haematococcus lacustris (Chlorophyceae, Chlamydomonadales, Haematococcaceae), a well-known algal species that is cultivated for industrial production of natural astaxanthin. Molecular and phylogenetic analyses allowed their genetic identification and revealed that these wild local strains belong to two different genera: Haematococcus and Dysmorphococcus (Chlorophyceae, Chlamydomonadales, Phacotaceae). Analysis of pigment extracts using High-Performance Thin Layer Chromatography and High-Performance Liquid Chromatography confirmed that the local strains of Haematococcus isolated were able to produce and accumulate astaxanthin under light and nutritional stress conditions. The local strains of Dysmorphococcus spp. were also able to produce astaxanthin. To our knowledge, this is the first time that these genera have been described in Reunion Island. The demonstration of the existence of local strains of Haematococcus is a promising first step toward the industrial production of natural astaxanthin in Reunion Island. Additionally, Dysmorphococcus spp. could represent an alternative source for high value carotenoids.