Dirofilaria immitis is the causative agent of canine heartworm disease, a severe health problem in dogs, especially in coastal areas of tropical and subtropical regions of the world. We employed molecular methods to investigate the occurrence of canine infection by filarioids in five municipalities of Baixada Fluminense (Magé, Duque de Caxias, Guapimirim, Nova Iguaçu, and São João de Meriti), a non-endemic area of Rio de Janeiro State, Southeast Brazil. A total of 110 canine blood samples collected from 2017 to 2018 and positive for microfilariae at the modified Knott’s test were screened by cPCR targeting DNA fragments of the 12S rDNA gene for filarial nematodes. Seventy-seven samples (70%) tested positive at the molecular analysis. Of these, 72 were identified as D. immitis and 5 (4.5%) as Acanthocheilonema reconditum. Dirofilaria repens was not detected in the studied municipalities of Baixada Fluminense. This is the first record of D. immitis and A. reconditum in the Baixada Fluminense region, Rio de Janeiro State, Brazil. The prevalence of D. immitis cases in the five municipalities suggests the establishment and maintenance of its enzootic cycle in the studied region, which indicate vulnerability to the occurrence of epidemic cycles and, possibly, human cases.