To meet the dietary requirements of a burgeoning human population, the demand for animal-dependent crops continues to grow. To meet the demand, intensive farming practices are used. The gains in food production associated with agricultural intensification may be offset by its detrimental effects on pollinator populations through natural habitat fragmentation and pesticide use. Abundance and species richness of pollinators have been found to decrease with increasing distance to natural habitat in agroecosystems, reducing crop yields. A key aspect of crop pollination lies in the diversity of functional traits (functional diversity, FD) of flower-visitor communities within crop fields. Higher FD allows improved pollination success through complementarity between flower-visitors’ morphology, phenology and behaviour. Many studies reported negative effects of increasing distance to natural habitats on the abundance and richness of flower-visitor communities, but the link between FD and natural habitat isolation is less well understood. Also, a more complete understanding of the functional traits of flower-visitor communities within crops should consider potential variations through time. Differences in resources availability between seasons are important in tropical areas and could modify ecological responses of flower-visitor communities to isolation. In this study, we surveyed the Hymenoptera and Diptera communities within mango orchards of South Africa using pan traps at 100 m, 200 m and at the maximal distance possible from any natural habitat. We measured the response of insect abundance, wing span and body size as well as functional diversity to habitat isolation during mango flowering (dry season), and during the wet season (after mango fruit harvest). Flying insect abundance decreased with increasing distance to natural habitat during mango flowering, but no effect was detected during the wet season. FD of flying insects declined with increasing distance to natural habitat in both sampling periods. Insects captured during mango flowering were smaller but had higher wing length/body length ratios than those caught during the wet season. This study highlights that mango orchards are more inhospitable for flying insects during mango flowering. This effect might be due to low palatability of mango flowers, or pesticide use in mango fields. In order to maintain a high FD of flower-visiting species, and reduce the detrimental effects of habitat isolation to ultimately ensure better crop pollination, we propose establishment of patches of resource-rich habitats combined with judicious use of pesticides within orchards.