Passiflora ovalis and P. contracta are species restricted to the Atlantic Rainforest (Mata Atlântica) of Brazil and were separated into two distinct taxonomic units based on different morphological traits, as inflorescence structure and indument, being the populations located between 7–19°S referred to P. contracta, while those found around 23°S belong to P. ovalis. Recently the species were grouped together under the specific name P. ovalis. The objective of this work was to understand the taxonomy of these species based in a Bayesian phylogenetic analysis using a combination of molecular markers from plastidial and nuclear genomes. The results confirmed the existence of two distinct species supported by full posterior probability values. We consequently propose accepting the two-species, which also have been validated both by morphologic differences and distinct geographic distribution.