Certain vector-borne organisms serve as etiological agents of equine disease. After previously identifying a new Ehrlichia species in horses from Mérida, we aimed to determine the infection frequency and screen for a wide range of vector-borne organisms from 93 tick-exposed, Ehrlichia seropositive horses in this region. PCR assays were performed to identify infection by organisms within the following genera: Anaplasma, Babesia, Bartonella, Ehrlichia, Leishmania, Mycoplasma, Neorickettsia, Rickettsia and Theileria. Overall, 90/93 horses (96.8%) were infected with one or more vector-borne organisms. Ninety (96.8%) horses were infected with Theileria equi and 21 (26.8%) with Babesia caballi. Nine (9.7%) horses were infected with the novel Ehrlichia species previously designated H7, reported in horses from Nicaragua and Brazil. Two horses (2.2%) were infected with Rickettsia felis. Anaplasma, Bartonella, Leishmania, Mycoplasma, or Neorickettsia species DNA was not amplified from any horse. Ticks collected from horses infected with vector-borne organisms were identified as Amblyomma cajennense sensu lato and Dermacentor nitens. Horses in Mérida are infected by a range of vector-borne organisms, including B. caballi, T. equi, Ehrlichia species H7, and R. felis. To the authors' knowledge, this constitutes the first report of molecular detection of R. felis in horses.