Pollination deficits in agricultural and natural systems are suggestive of large reductions in pollinator populations. However, actual declines are difficult to demonstrate using census data. Here, we show census data to be misleading because many abundant pollinators exhibit high levels of production of sterile diploid males usually found only in small inbred hymenopteran populations; Euglossa imperialis exhibits high levels of diploid male production induced by low effective population sizes (Ne ≈ 15), despite being the most abundant orchid bee in lowland tropical forests in Panama. We caution that although some pollinators appear abundant on the basis of census data, their long–term persistence may be highly tenuous based on genetic evidence. We propose the use of diploid male frequency data as a metric for assessing the sustainability of bee populations.