Studies on canine babesiosis in northeastern Brazil are scarce, although the weather conditions in this region are favorable for the development of the tick vector. This study determined the prevalence of Babesia vogeli in dogs sampled in Teresina, state of Piauí, northeast Brazil, using direct and indirect diagnostic methods and performed a phylogenetic analysis of 18S rRNA sequences. A total of 315 dogs were screened during routine care regardless of clinical suspicion. Blood was collected by jugular venipuncture to perform indirect immunofluorescence assay (IFA) and polymerase chain reaction (PCR) and for parasite screening in peripheral blood smears. Positivity was 2.2% (7/315) by microscopy, 4.8% (15/315) by PCR, and 48.6% (153/315) by IFA. PCR amplified a 602-bp fragment of the piroplasmid 18S rRNA gene, and sequence alignment and analysis revealed 99% homology with B. vogeli isolates from other regions of Brazil and other countries. In addition, there was high variability among sequences from other northeast states of Brazil. This study is the first to perform the molecular analysis of B. vogeli in Piauí. The results demonstrate that canine babesiosis is endemic in dogs sampled in Teresina and that PCR may be the method of choice to perform parasite screening in this region.