 In 1993, Géraldine Veron and François Catzeflis published a DNA hybridization study suggesting that the fossa was more closely related to mongooses (family Herpestidae) than to cats or civets. However, in 1995, Veron's morphological study once again grouped it with Felidae. In 2003, molecular phylogenetic studies using nuclear and mitochondrial genes by Anne Yoder and colleagues showed that all native Malagasy carnivorans share a common ancestry that excludes other carnivores (meaning they form a clade, making them monophyletic) and are most closely related to Asian and African Herpestidae. To reflect these relationships, all Malagasy carnivorans are now placed in a single family, Eupleridae. Within Eupleridae, the fossa is placed in the subfamily Euplerinae along with the falanouc (Eupleres goudoti) and Malagasy civet, but its exact relationships are poorly resolved.
