In Mexico, the distribution and the presence of pathogenic genospecies of B. burgdorferi in dogs and their ticks has not been extensively investigated. The study of canine borreliosis is acquiring greater relevance, since the dog is considered to be an important sentinel for pathogens pertaining to the complex Borrelia burgdorferi sensu lato; in addition, dogs could be playing a key role in the spread of ticks from forested areas into the domestic environment. This study aimed to detect and estimate the prevalence of B. burgdorferi s.l. in dogs and their ticks in two rural communities of Yucatán, Mexico. In each community, 50 houses were visited, where 144 blood samples from dogs were studied by puncture of the saphenous vein, as well as the collection of their ticks. To detect the presence of B. burgdorferi s.l. in these samples, the conserved gene flaB, p66 and ospC were PCR amplified. A total of 144 dog blood samples, and 846 of ticks were obtained from the examined animals. Considering tick species, Rhipicephalus sanguineus sensu lato (786 / 846) was common, while Ixodes affinis (33 / 846), and Amblyomma mixtum (27 / 846) resulted less frequent. As per gene conservation, the prevalence of B. burgdorferi in canine blood was 17.3 % (25 / 144) to flaB, 12.50 % (18 / 144) for p66 and 1.38 % (2 / 144) for the ospC gene. Within the analyzed ticks, R. sanguineus s.l. had a prevalence of 0.89 %, A. mixtum 5.88 % and I. affinis 15.15 %, being this last species the one that presented higher prevalence. Two dogs and their ticks I. affinis were positive to the flaB gene. Only a tick R. sanguineus s.l. was positive to the gene p66 and no tick species was positive the ospC gene. This study confirmed the existence of B. burgdorferi s.l. in dogs and their ticks in rural communities of Yucatán, Mexico. The detection of Borrelia in dogs may be an important criterion for the evaluation of the risk of borreliosis in humans, since the dog can be used as an epidemiological indicator for the identification of new outbreaks of this disease.