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Background: Vector-borne diseases are emerging worldwide and have an important zoonotic relevance. In the last few years, the interest in vector-borne pathogens in cats has increased. However, studies on feline vector-borne pathogens on tropical islands are lacking. Islands differ from continental countries because they have an enclosed population of animals, with all year presence of the vectors and, most often, without vector control measures. This study focused on the molecular identification and phylogenetic analysis of vector-borne pathogens in autochthonous cats with a mixed indoor–outdoor lifestyle from Maio Island, Cape Verde archipelago. Methods: Blood samples were collected from 80 asymptomatic cats, representing almost a quarter of the total cat population of the island. The presence of DNA of protozoa of the genus Hepatozoon and bacteria belonging to family Anaplasmataceae and to genus Bartonella was assessed by PCR and phylogenetic analysis was conducted. Statistical analysis was performed to identify risk factors associated with infection. For feline hepatozoonosis, a worldwide dataset of Hepatozoon felis sequences retrieved from mammal species and vectors along with Hepatozoon spp. sequences retrieved from felids was generated, phylogenetically analyzed and the geographical and host distribution was assessed. Results: Hepatozoon felis genotype I was identified in 12 (15%) cats from Maio Island whereas none of the cats were PCR positive for the other pathogens tested. No significant association of H. felis infection with age, sex, location or presence of vectors was observed by statistical analysis in Cape Verde's cats. Phylogenetic analysis on the worldwide dataset of feline Hepatozoon sequences showed two significant distinct clades for H. felis genotype I and II. Different geographical distributions were assessed: H. felis genotype I was the only genotype found in Africa and has been reported worldwide, with the exception of Japan and Brazil where only H. felis genotype II has been reported. Conclusions: The identification of H. felis genotype I in cats in Maio Island highlights the need to further investigate the significance of H. felis genotypes and to clarify the epidemiological aspects of this infection. [ABSTRACT FROM AUTHOR]