Within the family Cambaridae, the genus Procambarus is especially important due to the number of species it contains and its wide distribution in the American Continent. Procambarus (Austrocambarus) llamasi is endemic to the Yucatan Peninsula, distributed in epicontinental water bodies, including lakes, marshes and flood plains, which may be relatively isolated. Due to the fragmented nature of its habitat, it might be expected to find highly structured populations with unique haplotypes. To describe the genetic variation of the different populations of P. llamasi and their distribution pattern, a phylogeographic analysis was performed using the mitochondrial COI gene. A 643 base pair fragment was sequenced from 53 individuals of ten populations. Different haplotypes were identified and a haplotype network was built using statistical parsimony for nested clade analysis. A total of 14 variable sites were found, 12 of which were informative; all nucleotide changes were transitions and nucleotide diversity was π = 0.0045. Ten haplotypes were found with a diversity of HD = 0.532, with one of them widely distributed. The nested clade analysis shows that current haplotypes are the result of a contiguous range expansion, suggesting that the source of the expansion was at the southern portion of the peninsula. This may occur due to the seasonal floodings in the region, which can create temporary connections between populations.