It is essential to understand the patterns of pollen dispersal in remnant vegetation occupying highly disturbed landscapes in order to provide sustainable management options and to inform restoration programs. Direct and indirect methods of paternity analysis were used to detect genetic contamination via inter-subspecific pollen dispersal from a planted stand of nonlocal Acacia saligna ssp. saligna (ms) into remnant roadside patches of local A. saligna ssp. lindleyi (ms). Genetic contamination was detected in 25.5% (indirect paternity assignment) to 32% (direct paternity assignment) of ssp. lindleyi progeny and occurred over a distance of 1.6 km. The results support studies that suggest genetic continuity is maintained by high levels of pollen dispersal in temperate entomophilous species. The results also indicate that patchily distributed remnant populations may be exposed to substantial amounts of genetic contamination from large-scale restoration with native taxa in the highly fragmented agricultural landscape of southern Western Australia. Management practices to reduce the risk of genetic contamination are considered.