Disruption of gene flow following anthropogenic fragmentation of natural habitat has been investigated in many species; however, fragmentation-induced effects on endemic plants that rely on species-specific invertebrate pollinators are still unclear. While honeybees can forage over long distances, many native bees with small body size are unable to extend their foraging range and overcome man-made infrastructure, making habitat fragmentation the largest threat to such systems. In many long-lived plants, the time since fragmentation has not been long enough for detectable changes in the genetic composition of standing populations, and changes in dispersal patterns observed in seeds may provide insights into the future impact of habitat changes. Using paternity assignment analysis, we characterised the plant mating system and changes in dispersal patterns across multiple fragmented and non-fragmented populations. Results showed that while pollen could travel unimpeded through unfragmented bushland, fragments separated by built-up areas resulted in complete isolation, with no pollen immigration. Native pollinators appeared unable to maintain an adequate inter-population pollen flow in heavily fragmented landscapes. This reduction in contemporary gene flow may reduce the ability of small populations to recover lost genetic variation through connection with larger remnants, with impacts on the future persistence of threatened species that rely on species-specific pollinators. Our study highlights the importance of understanding species-specific life history and ecological traits when planning conservation actions, such as translocations and reintroductions, in order to maintain, or increase, adequate population size to sustain genetic diversity and mating systems within populations.