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Genetic diversity and haplotype composition of the West Indian manatee (Trichechus manatus) population from the San San Pond Sak (SSPS) wetland in Bocas del Toro, Panama, was studied using a segment of the mitochondrial DNA (control region). No genetic information to date has been published for manatee populations in Panama. Due to the secretive behavior and small population size of the species in the area, DNA extraction was conducted from opportunistically collected fecal (N = 20), carcass tissue (N = 4), and bone (N = 4) samples. However, after DNA processing, only 10 samples provided enough quality DNA for sequencing-three fecal, four tissue, arid three bone samples. We identified three haplotypes in total: J01. was previously published (N = 3), while the other two haplotypes, J02 (N = 3) and J03 (N = 4), are reported for the first time. The genetic diversity was similar to previous analyses conducted in the Caribbean with moderate values of nucleotide (pi = 0.00152) and haplotypic (Hd = 0.57) diversity Connectivity assessment between the SSPS population with published range-wide manatee haplotypes was based on sequence similarity, genetic distance, and genetic differentiation. The identified J01 haplotype is also found in populations to the north along the Central American and Gulf of Mexico coasts indicating reduced differentiation (Fst = 0.0094). In contrast, comparisons between SSPS sequences and South American populations (not including Colombia), the West Indies, and Florida showed fewer similarities (Fst = 0.049 and 0.058, respectively). These results corroborate previous phylogeographic patterns already established for manatee populations and situate the manatee population in Panama within the Belize/Mexico cluster. In addition, these findings provide a baseline for comparative studies of manatees in other areas of Panama and Central America. These results can assist with management decisions regarding conservation of genetic diversity, future introductions, connectivity, and effective population size of manatee populations along the Central American corridor.