This study presents the first comprehensive genetic analyses of common bottlenose dolphin (Tursiops truncatus) based on mitochondrial DNA and microsatellite loci in the Wider Caribbean. Live captures of bottlenose dolphins have been occurring since the turn of the 20th century in Wider Caribbean waters where little is known about their population structure and genetic diversity. In this study, blood or tissue samples were obtained from stranded or captive dolphins from nine geographic regions. One hundred fifty-eight sequences of the mitochondrial DNA control region and nine microsatellite loci were analyzed and compared with previously published sequences. This study revealed the presence of ‘inshore’ ecotype and ‘worldwide distributed form’ haplotypes of bottlenose dolphins in Wider Caribbean waters. At the mitochondrial level, genetic differentiation between these two groups was significant (FST = 0.805, P < 0.001). Analyses of mitochondrial DNA sequences at a wider geographic level revealed three genetically differentiated (FST = 0.254, ΦST = 0.590, P < 0.001) population units: Puerto Rico, Cuba/Colombia/Bahamas/Mexico, and Honduras. There was evidence of low female-mediated gene flow among these population units (Nmf = 1.46). Microsatellite analyses identified four somewhat different population units: Honduras/Colombia/Puerto Rico, Bahamas, Cuba and Mexico. The presence of ‘worldwide distributed form’ and ‘inshore’ ecotype haplotypes in particular population units, may be causing differences in the population structure pattern showed by each molecular marker. Decreased observed heterozygosity and three loci out of the Hardy–Weinberg equilibrium were found in the Honduras/Colombia/Puerto Rico population unit suggesting a Wahlund effect. The genetic differentiation and divergence between the two forms identified in this study must be taken into consideration for captive programs that aim to reproduce bottlenose dolphins from this region. Although genetic diversity at the mitochondrial and microsatellite level in these dolphins seems to be relatively high, additional demographic and abundance data must be obtained before more captures are allowed.