Despite increasing recognition of the importance of the multiple dimensions of biodiversity, including functional or genetic diversity as well as species diversity, most conservation studies on ecosystem service-providing insects focus on simple diversity measures such as species richness and abundance. In contrast, relatively little is known about the genetic diversity and resilience of pollinators or natural enemies of crop pests to population fragmentation and local extinction. The genetic diversity and demographic dynamics of remnant populations of beneficial insects in agricultural areas can be a useful indicator proving additional insights into their conservation status, but this is rarely evaluated. Although gene flow between agricultural and seminatural areas is key to maintaining genetic diversity, its extent and directionality remain largely unexplored. Here, we apply a pan-European sampling protocol to quantify genetic diversity and structure and assess gene flow between agricultural and nearby seminatural landscapes in populations of two key ecosystem service-providing insect species, the lady beetle Coccinella septempunctata, an important predator of aphids and other crop pests, and the bee pollinator Andrena flavipes. We show that A. flavipes populations are genetically structured at the European level, whereas populations of C. septempunctata experience widespread gene flow across the continent and lack any defined genetic structure. In both species, we found that there is high genetic connectivity between populations established in croplands and nearby seminatural areas and, as a consequence, they harbor similar levels of genetic diversity. Interestingly, demographic models for some regions support asymmetric gene flow from seminatural areas to nearby agricultural landscapes. Collectively, our study demonstrates how seminatural areas can serve as genetic reservoirs of both pollinators and natural enemies for nearby agricultural landscapes, acting as sources for recurrent recolonization and, potentially, contributing to enhancing ecosystem service and crop production resilience in the longer term.