Understanding how restoration and land management practices may impact the structure of native bee communities is important especially considering reported global bee declines. I assessed bee community and vegetation composition in tallgrass prairie and oak savanna, some of the most endangered and biodiverse habitats in Canada. I found distinct differences in bee abundance and diversity among land management types, with remnant sites in most cases having comparably low bee diversity. This was driven by differences in floral abundance, canopy cover, and presence of woody debris. Bee community composition was unique at each locality, and I documented several bee species for the first time in Canada. I also found more bumble bee colonies and greater floral resources at restored compared to remnant sites using non-lethal DNA sampling and microsatellite markers to estimate colony densities. Linking landscape structure with use will improve habitat management and bee conservation in this rare habitat.