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The global conservation status of the bottlenose dolphins (Tursiops truncatus) by the IUCN is as “Least Concern”. However, bottlenose dolphins seem to form a global metapopulation consisting of a widely distributed genetic form (“worldlwide”) and many localized “inshore forms” that live relatively isolated in small populations and that are more at risk of decline and extinction due to their overlap with human activities. In this study we used previously published data from bottlenose dolphins in the Caribbean to assess the degree of genetic isolation of bottlenose dolphins from Bocas del Toro (BDT), Panama. A previous study found a described a unique mtDNA haplotype for this population, not found anywhere else in the Caribbean, suggesting high degree of isolation. Using microsatellites data we compared the BDT population to the neighboring population in Costa Rica and other populations in the Caribbean. Our finding support that BDT dolphins are isolated from other Caribbean populations, and that despite no photoID evidence there is small genetic flow from Panama to Costa Rica. This population is threaten by intense dolphin watching that is affecting their foraging time, communication, and even causing death due to collisions with boats. The whale-watching Resolution ADM/ARAP NO. 01 was established 8 years ago, but there is neither enforcement nor a transparent certification process. The dolphin Bocas urgently need the Panamanian government to follow their commitment to protect their marine mammals.