Paradoris adamsae sp. nov. is described based on three specimens collected in Bocas del Toro, on the Caribbean coast of Panama. The new species is clearly a member of Paradoris because of the presence of a jaw with three plates, a narrow radula, a grooved outer edge of the lateral tooth hook, and grooved oral tentacles. It differs from other members of the genus by having a relative large body size, brownish body color, small rhinophores, and high rounded tubercles on the mantle. This is the second record of the genus Paradoris in the western Atlantic, where Paradoris mulciber has been reported from Brazil, Costa Rica, and the Caribbean Sea. A phylogenetic analysis including 25 taxa shows that Paradoris is monophyletic and divided into two main clades, one containing all tropical eastern Pacific, tropical Atlantic, and Mediterranean species, which is sister to a clade composed of tropical and temperate Indo-Pacific species. In the Indo-Pacific clade, three taxa from the southern temperate seas are sisters to the rest of the Indo-Pacific species. According to the present phylogenetic hypothesis, P. adamsae sp. nov. is more close related to Paradoris lopezi Hermosillo & Valdes, 2004, from the tropical eastern Pacific than to P. mulciber, from the western Atlantic. The present phylogeny is similar in several regards to hypotheses proposed for other groups of opisthobranchs and other marine organisms and suggests that the same major vicariant events had affected the biogeography of these groups. As a result of the present study at least 16 distinct species can be recognized in Paradoris, more than the double the number of valid species cited in the last revision of the genus.