Background. The captive cetacean industry is very profitable and popular worldwide, focusing mainly on leisure activities such as "Swim-with-dolphins" (SWD) programs. However, there is a concern for how captivity could affect the bottlenose dolphin Tursiops truncatus, which in nature is a highly social and widespread species. To date, there is little information regarding to the impact of restricted population size on their genetic structure and variability. Methods. The aim of this study was

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... estimate the genetic diversity of a confined population of T. truncatus, composed of wild-born (n=25) from Cuba, Quintana Roo and Tabasco, and captive-born (n=24) dolphins in southern Mexico, using the hypervariable portion of the mitochondrial DNA and ten nuclear microsatellite markers: TexVet3, TexVet5, TexVet7, D18, D22, Ttr19, Tur4_80, Tur4_105, Tur4_141 and GATA098. Results. Exclusive mtDNA haplotypes were found in at least one individual from each wild-born origin populations and in one captive-born individual; total mean haplotype and nucleotide diversities were 0.912 (±0.016) and 0.025 (±0.013) respectively. At microsatellite loci, low levels of genetic diversity were found with a mean number of alleles per locus of 4 (±2.36), and an average expected heterozygosity over all loci of 0.544 (±0.163). Measures of allelic richness and effective number of alleles were similar between captive-born and wild-born dolphins. No significant genetic structure was found with microsatellite markers, whereas the mtDNA data revealed a significant differentiation between wild-born organisms from Cuba and Quintana ROO. Discussion. Data analysis suggests the occurrence of a recent genetic bottleneck in the confined population probably because of a strong founder effect, given that only a small number of dolphins with a limited fraction of the total species genetic variation were selected at random to start this captive population. The results herein provide the first genetic baseline information on a captive bottlenose dolphin population in Mexico.