The genetic structure of populations of the tick Amblyomma ovale from five distinct areas of the Brazilian Atlantic rainforest was evaluated via DNA sequencing and associated with the presence of domestic dogs acting as hosts at the edge of forest fragments. Ticks were collected from domestic dogs and from the environment between 2015 and 2017. Four collection areas were located in the surroundings and within the Serra do Mar State Park, São Paulo State (23°37′21"S, 45°24′43"W), where dogs were bimonthly monitored along 2 years using camera traps and GSM trackers. To determine the spatial limits of genetic structure, ticks collected upon dogs living near the Serra do Baturié, Ceará State (4°15′40"S, 38°55′54"W) were included as well. A total of 39 haplotypes of 16S rRNA and Cox 1 mitochondrial genes sequences were observed, with 27 of them coming from areas within the Serra do Mar State Park. No haplotype was shared between the Serra do Mar and the Serra do Baturié indicating isolation of tick populations at the scale of 2000 km. Although three different haplotype lineages of A. ovale occurred within the Serra do Mar State Park, no genetic structure was found across the study sites within this park, suggesting high tick gene flow across a range of 45 km. Monitoring data from domestic dogs and wild carnivores showed that these species share the same habitats at the forest edge, with dogs playing a likely limited role in tick dispersal. Our findings have important implications for understanding the genetic structure of wide spread A. ovale along Brazilian rainforest remnants, which can further be associated to tick-borne infectious agents, such as Rickettsia parkeri, and used for predicting future patterns of tick diversity in the Brazilian Atlantic rainforest.