Arthropod-borne diseases are important causes of morbidity and mortality of companion animals in Trinidad. As clinical signs are vague, more sensitive methods to diagnose these diseases based on the polymerase chain reaction (PCR) followed by reverse line blot hybridization (RLB) of amplified products are being developed. An RLB of 14 oligonucleotide probes coupled with polymerase chain-amplified regions of 16S rRNA or 18S rRNA genes of hemoparasites from cats and dogs detected Ehrlichia canis, Anaplasma platys, Babesia canis vogeli, feline mycoplasmas ("Candidatus Mycoplasma haemominutum," Mycoplasma haemofelis), and some unknown species within the Babesia/Theileria group and the Anaplasma/Ehrlichia tribe. Amplified products were obtained from blood samples collected from 348 dogs and 15 cats. Overall, hemopathogen DNA was detected in 92 (26.4%) dogs and six (40.0%) cats. E. canis (49, 14.1%) and feline mycoplasma (5, 33.3%) DNA were most frequently identified in dogs and cats, respectively. B. canis vogeli (1, 6.7%) and E. canis (1, 6.7%) were also detected in cats. Mixed infections of Anaplasma/Ehrlichia sp. and Babesia sp. were present in five (1.4%) dogs, while mixed infections of the feline mycoplasmas were present in two (13.3%) cats, one of which was also positive for E. canis. Pyrexia was significantly associated with a positive RLB result in dogs (P = 0.00, χ2, 1 df). This is the first reported application of macro-arraying techniques to detect arthropod-borne hemopathogens of companion animals in the Americas and the first detection of DNA of B. canis vogeli and E. canis in cats in Trinidad.