Reliable abundance estimates are critical for management and conservation of coastal small cetaceans. This is particularly important in developing countries where coastal human populations are increasing, the impacts of anthropogenic activities are often unknown, and the resources necessary to assess coastal cetaceans are limited. We adapted ship-based line transect methods to small-boat surveys to estimate the abundance of bottlenose dolphins (Tursiops truncatus) at Turneffe Atoll, Belize. Using a systematic survey design with random start and uniform coverage, 34 dolphin clusters were sighted during small-boat line transect surveys conducted in 2005–2006. Distance sampling methods estimated abundance at 216 individuals (CV = 27.7%, 95% CI = 126–370). Due to species rarity in the Atoll, small sample size, and potential violations in line transect assumptions, the estimate should be considered preliminary. Nevertheless, it provides up-to-date information on the status of a regional population in an area under increasing threat of habitat loss and prey depletion via uncontrolled development and unsustainable fishing. This information will be useful as Belize develops a new conservation initiative to create a comprehensive and resilient marine protected area system. Our study illustrates the application of distance sampling methods to small-boat surveys to obtain abundance estimates of coastal cetaceans in a region lacking resources.