Based on previously published data, the Czech Republic is regarded an endemic country of the onchocercid nematodes Dirofilaria immitis (Leidy, 1856) and Dirofilaria repens Railliet et Henry, 1911. Nevertheless, while cases of D. repens are commonly reported from dogs in South Moravia, no recent records of D. immitis are available. Therefore, the present study was performed to clarify the occurrence of both species of Dirofilaria Railliet et Henry, 1910. Blood samples of 551 dogs sampled during 2015 and 2016 were analysed microscopically for presence of microfilariae and blood sera were examined by IDEXX SNAP® 4Dx® test (IDEXX, USA). DNA from blood of microscopically positive dogs was extracted and PCR protocol amplifying fragment of cytochrome c oxidase I (COI) gene was performed; PCR products were then sequenced. All dogs from the Bohemian part of the Czech Republic were negative. The prevalence of D. repens in the Moravian region was 5.7 % (27/476). BLAST analyses of obtained sequences confirmed the presence of D. repens (99-100% identical to KX265049). All sampled animals showed a negative result for D. immitis antigen in IDEXX SNAP® 4Dx® test. Our study confirmed the previously reported occurrence of D. repens in South Moravia and revealed its spreading from the epicentre to the north and west. PCR with subsequent sequencing together with negative results for D. immitis antigen in IDEXX SNAP® 4Dx® test revealed only D. repens infection. A previously published autochthonous infection of dogs with D. immitis in South Moravia was not confirmed.