Bees, including bumblebees, are highly valued for the pollination services they provide to natural ecosystems and agricultural crops. However, many bee species are facing declines, likely a result of habitat loss, pesticide use and climate change. Additionally, the use of imported commercial bumblebee colonies for crop pollination poses several risks to wild pollinators, including competition, hybridisation and pathogen spillover. A stock-take is needed of wild bees on both genetic and functional levels to identify vulnerable populations, detect local adaptations and to prevent further pollinator losses. We examine wild Irish B. terrestris ssp. audax on genomic, proteomic, and behavioural levels with reference to British and commercial populations to deepen our understanding of the selective processes acting on wild and domesticated bumblebee populations. We find that wild Irish and British populations of B. t. audax are distinctive on genomic levels and exhibit differential signatures of selection. We also find putative evidence for genetic distinctions between wild and commercial populations. A genomic examination of canonical immune genes in wild, Irish bumblebees highlighted several genes undergoing positive, purifying and possibly balancing selection, possibly reflecting their functional diversity and indicating recent adaptation. We uncover distinctions in the proteomes of wild and commercial lineages of lab-reared worker bee fat bodies and brains, as well as in the proteomic responses of these organs to pesticide exposure and infection. Finally, distinctions in the growth dynamics of wild and commercial lineages of B. t. audax colonies were identified alongside differences in the bacterial and fungal gut microbiomes of lab-reared wild and commercial workers. Overall, the findings of this thesis provide novel insights into the genetic, physiological, and behavioural distinctions between wild and domesticated populations of B. t. audax which will likely have major implications for how we conserve valuable genetic resources and manage commercial bumblebee imports.