The native prairie of the southern Great Plains has been especially modified by two related forces: conversion of native prairie to agricultural forms of land use and removal of black-tailed prairie dogs (Rodentia: Sciuridae, Cynomys ludovicianus (Ord, 1815)) that act as ecosystem engineers via their burrowing and grazing activities. It is unknown how these changes have affected the native bee community. We surveyed the bee communities in relatively intact native prairie at two National Wildlife Refuges in Texas, quantifying bee community structure as a function of the presence/absence of grazing by prairie dogs. Over a 5-mo sampling period in spring-summer 2013, we found high overall bee diversity (180 species, mostly solitary ground-nesters), with differences detected in diversity between Muleshoe and Buffalo Lake National Wildlife Refuges as well as on and off prairie dog colonies. Although the same three species dominated the bee community at both refuges, most species were represented by relatively few individuals, leading to overall differences in diversity (richness, evenness, and effective number of species) by refuge. Bee diversity differed between sites on and off prairie dog colonies, but in trends that differed by refuge and by index, suggesting that location was more important than prairie dog presence.These results represent a reference fauna against which other regional bee communities in other land-cover types can be compared, but the high spatial heterogeneity we found indicates that detecting effects of landscape change on native bees will be challenging.