Among the fiddler crabs from the Americas, Uca panamensis (Stimpson, 1859) (Crustacea: Decapoda: Ocypodidae) is unusual in its behavior and ecology, living in stony habitats rather than sandy or muddy substrates. This species also has several unusual morphological characters of the carapace and major and minor chelae, and had been placed in either the subgenera Minuca Bott, 1954, or Leptuca Bott, 1973. The armature at the inner corner of the orbital floor, as well as the morphology of the urocardiac ossicles of the gastric mill of U. panamensis, are, however, plesiomorphic characters, and are closer to the condition in species belonging the subgenera Uca and Afruca. Phylogenetic relationships, based on mitochondrial 16S rDNA and cytochrome oxidase subunit I, and nuclear 28S rDNA, supported by its unusual morphological features indicate that this species belongs to its own subgenus. A new subgenus Uca (Petruca) subgen. nov. is herein established for U. panamensis. In addition, the status of Uca thayeri Rathbun, 1900, U. umbratila Crane, 1941, U. virens Salmon & Atsaides, 1968, and U. longisignalis Salmon & Atsaides, 1968, are revised and discussed based on a reappraisal of their phylogenetic relationships.