Three major flyways of the Nearctic – Neotropical bird migration system converge at the coastal plains of the Isthmus of Tehuantepec, Mexico. Approximately one million vultures and raptors traverse the area during the autumn migration season, and more than 60 species of nocturnally migrating birds have been recorded there. Furthermore, more than 60 bat species inhabit this region, which also harbors the most important wind resource area of the country. There, the number of wind turbines increased from 98 to >1500 between 2006 and 2015. We estimated bird and bat mortality at three wind farms in the Isthmus, correcting for different sources of bias. Between June and November 2015, we found 75 bird and 72 bat carcasses, belonging to 30 and 20 species respectively. Although we found more bird than bat carcasses, our corrected estimates are higher for bats than for birds. Corrected mortality ranges between 4.0 and 5.6 birds/MW and 8.9–21.4 bats/MW during the months of the study, or between 9.18 and 12.95 birds/MW/year and 20.44–43.67 bats/MW/year. Contrary to patterns of aerial vertebrate mortality at wind farms in temperate latitudes, all bat and most bird fatalities were from resident species, even when considering bird migration months only. Corrected bird mortality was highest at the wind farm with the tallest wind turbines. Our estimated fatalities/MW/year are higher than rates of bat and bird mortality recorded at numerous wind farms in the United States, and our estimates may still be biased low. Thus, our results offer a first glimpse to the magnitude of bird and bat mortality at this tropical hotspot for aerial vertebrates. More than 15 wind farms are currently operating in the region, hence a larger-scale effort is needed to fully understand the cumulative mortality of aerial vertebrates, particularly of resident species, at this wind energy hub and diversity hotspot.