The endosymbiotic bacterium Wolbachia is a promising tool for controlling arboviral diseases transmitted by the mosquito Aedes aegypti, and can spread by itself through wild mosquito populations following local introductions. Recent Wolbachia introductions into Ae. aegypti populations in Cairns, Australia, have produced a slower than anticipated spread that could be due to: i) non-perfect transmission of Wolbachia from mother to offspring; ii) dispersal being leptokurtically biased towards long distances in Ae. aegypti adults; and iii) geographical barriers to Ae. aegypti dispersal. We investigated these three potential causes using double-digest restriction-site associated DNA sequencing and Wolbachia screening in 161 Ae. aegypti collected from Cairns in 2015. We detected differential Wolbachia status among full siblings in one out of 10 Wolbachia-infected matrilineages, providing the first evidence for transmission failure in this host/Wolbachia system. Full-siblings were also found in ovitraps up to 1312 m apart, indicating a potential for long-distance movement in Ae. aegypti females that are generally considered weak dispersers. We also detected a small but significant barrier effect of Cairns highways on Ae. aegypti dispersal using distance-based redundancy analysis (dbRDA) and a patch-based simulation analysis. These findings together may explain the slow spread of Wolbachia infection through the Ae. aegypti population in Cairns, and highlight the utility of genome-wide SNPs for fine-scale ecological investigations. Our approach could be extended to other host/Wolbachia systems that are increasingly considered for the biocontrol of disease vectors and pests.