The genus Bocaparvovirus (BoV) in the subfamily Parvovirinae shows a wide host spectrum and causes infection with different clinical findings in various animals. In recent years, canine and feline Bocaparvovirus infections, which are novel parvovirus species, have been reported in different geographical regions. The aim of this study is to investigate the presence of canine and feline Bocaparvovirus genotypes in dog and cat fecal samples and to perform their molecular characterization. The presence of canine and feline bocaparvovirus nucleic acid was investigated in stool samples taken from 74 dogs and cats. After PCR tests, it was found that five out of 46 dogs were positive for CBoV-1 and five out of 46 dogs were positive for CBoV-2, while two out of 28 cats were positive for FBoV-2. The sequence comparison of the capsid protein gene (VP2) of the five CBoV-1 identified in this study shared a high identity with each other (96.4-99.2% nt and 94.6–99.2% aa identities) and with previously reported CBoV-1 strains (93.4-98.9% nt and 93.9–100% aa identities). It was determined that five CBoV-1 strains were located in Lineage 2 in the phylogenetic map. The nucleotide and amino acid comparison showed that the non-structural protein (NS1) gene sequences of the five CBoV-2 strains identified in this study shared a high identity with each other (93.5-97.0% nt and 93.6–100% aa identities) and with previously reported CBoV-2s (92.2–98.6 % nt and 92.8–100% aa identities). The phylogenetic map showed three strains (OR690113, OR690112, OR690117) in Lineage 1 and two strains (OR690114, OR690115) in Lineage 2. The sequence comparison of the nuclear phosphoprotein-1 (NP1) gene sequences of the two FeBoV strains identified in this study shared identity with each other (100% nt and aa identities) and with previously reported FeBoV strains (63.8-99.5% nt and 59.4–100% aa identities). As a result of the sequence analysis, it was determined that the two FBoV-2 strains identified in the study were included in Lineage 1. Findings of the present study compile current genetic data and contribute to the molecular epidemiology of these infections. It is recommended to evaluate Bocaparvoviruses, use molecular methods and conduct further studies on the diagnosis of infections in dogs and cats.