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Bartonella spp. and haemoplasmas are pathogens of veterinary and medical interest with ectoparasites mainly involved in their transmission. This study aimed at molecular detection of Bartonella spp. and haemoplasmas in cats (n = 93) and dogs (n = 96), and their related fleas (n = 189) from countries in East and Southeast Asia. Ctenocephalides felis was the dominant flea species infesting both cats (97.85%) and dogs (75%) followed by Ctenocephalides orientis in dogs (18.75%) and rarely in cats (5.2%). Bartonella spp. DNA was only detected in blood samples of flea-infested cats (21.51%) (p < .0001, OR = 27.70) with Bartonella henselae more frequently detected than Bartonella clarridgeiae in cat hosts (15.05%, 6.45%) and their associated fleas (17.24%, 13.79%). Out of three Bartonella-positive fleas from dogs, two Ct. orientis fleas carried Bartonella vinsonii subsp. berkhoffii and Bartonella clarridgeiae, while the 3rd flea (Ct. felis) carried Candidatus Bartonella merieuxii. Felines represented a risk factor for Bartonella spp. infections, where fleas collected from cats (32.25%) presented an increased likelihood for Bartonella spp. occurrence (p < .0001, OR = 14.76) than those from dogs (3.13%). Moreover, when analysing infectious status, higher Bartonella spp. DNA loads were detected in fleas from bacteraemic cats compared to those from non-bacteraemic ones (p < .05). The haemoplasma occurrence was 16.13% (15/93) and 4.17% (4/96) in cat and dog blood samples from different countries (i.e. Indonesia, Malaysia, the Philippines, Taiwan and Thailand), with cats more at risk of infection (p < .01, OR = 5.96) than dogs. Unlike Bartonella spp., there was no evidence for flea involvement in the hemoplasmas' transmission cycle, thus supporting the hypothesis of non-vectorial transmission for these pathogens. In conclusion, client-owned cats and dogs living in East and Southeast Asia countries are exposed to vector-borne pathogens with fleas from cats playing a key role in B