Canine dirofilariasis is common in Brazil, but molecular diagnosis is rare even though molecular studies increase our knowledge about molecular epidemiology and circulating genotypes from helminths worldwide. This study aims to estimate the prevalence of infection with a modified Knott's test and to perform molecular characterization of Dirofilaria immitis (Leidy, 1856) Railliet and Henry, 1911, in dogs from endemic areas of Maricá and Niterói municipalities, Rio de Janeiro State, Brazil. Molecular characterization was performed in 33 blood samples from dogs positive for microfilariae and 4 adult worms obtained from 2 other dogs. DNA extraction followed by PCR for mitochondrial target 12S rDNA and cytochrome oxidase subunit 1 (COI) of D. immitis were performed, and the amplified products were sequenced. All sequences were identical for both gene targets and showed 100% identity with D. immitis sequences from different animal species from various countries. The study concluded that this genotype of D. immitis might be dispersed worldwide.