Abstract Recent studies have contributed to a better understanding of the circumscription of some genera of Malpighiaceae and the overall diversity of the family in Brazilian tropical ecosystems. In southern Brazil, however, this important group of lianas and shrubs still has not been fully categorized. The present study provides identification keys based on floral and fruit morphology for the 23 genera reported from southern Brazil. The importance of the number of styles and the position and shape of the stigmas for the recognition of genera was confirmed. Illustrations of morphological characteristics used in the keys and notes about taxonomy, species richness and distribution are provided. It should be noted that the occurrence of some Malpighiaceae genera that are represented by only one species in the southern region, such as Bronwenia, Camarea and Heladena, are not yet cited in the Flora do Brasil 2020 database. A total of 95 species were confirmed and documented by voucher specimens. Banisteriopsis pseudojanusia, Heteropterys dusenii and Peixotoa catarinensis, occur exclusively in southern Brazil and are classified as “Critically Endangered”, “Vulnerable” and “Endangered” in the Brazilian Red List, respectively.