Although habitat fragmentation and agricultural intensification are known as threads to pollinator diversity, little is known about consequences for population size and genetic diversity. Here, we combined detailed field observations, molecular approaches and GIS-based quantification of landscape structure (measured by proportions of seminatural habitats and proportions of mass flowering crops) to get new insights into driving forces of population dynamics of the bumblebee species Bombus pascuorum. Comparing 13 agriculturally dominated landscape sectors, we found the proportion of mass flowering crops to positively influence bumblebee abundance whereas the proportion of seminatural habitats was of minor importance. We used microsatellites to quantify landscape-related colony densities, inbreeding and population substructure. Detected colony densities did not correlate with landscape parameters or with local worker abundance, measured by field observations. These results indicate that increased worker abundances within landscapes are rather due to greater colony sizes than due to an increased number of nests. We found significant population substructure, measured by FST and seven landscape sectors to bear significantly increased inbreeding values (FIS). FIS was strongly varying between sectors but did not correlate with landscape structure. Moreover, FIS had a significantly negative effect on colony size, demonstrating the importance of genetic diversity on population fitness at a landscape scale. We suggest that inbreeding levels might be related to the temporal variation of food resources and population sizes in agricultural landscapes.