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The genus Pristimantis is highly diverse in the tropical forests of Central America, presenting a wide morphological variety, which makes its classification very difficult. Therefore, molecular techniques are currently required to aid in understanding the genetic relationship of the genus. The following study attempts established a Bayesian inference analysis to understand the speciation modeling processes of the genus Pristimantis between Costa Rica, Panama, and Colombia. For this purpose, the programs MEGA, BEAST2, and FigTree were used using COI genes from the NCBI GenBank to study the evolutionary relationships between populations of the genus Pristimantis. As a result, highly significant Bootstrap values ??were obtained at the nodes of some species (>90%), confirming the reliability of the evolutionary relationships obtained and a possible past or ongoing speciation. Bayesian inference showed that the species P. cruentus (Copé, Coclé), P. cerasinus (Valle de Antón, Coclé), and P. museosus (Santa Fe, Veraguas, and Copé, Coclé) presented clades with very close groupings and shorter branches, which shows signs of a more recent speciation in this group. Furthermore, the population of P. museosus in Limón, Costa Rica, presents greater genetic divergence with respect to the central populations of Panama, most likely due to the isolation of the Talamanca Mountain range. Similarly, the populations of P. gaigei in Antioquia and Panama reveal distinct clades with considerable genetic divergence, possibly due to separation by important geographical barriers such as the Andes Mountains and the Isthmus of Panama itself.