Anaplasma and Ehrlichia species are important tick-borne pathogens that cause disease in cattle, dogs, horses and humans; with little information available about these agents in Colombia. The aim of this study was to provide molecular evidence for the presence of Anaplasma sp. and Ehrlichia sp. species in ticks collected from horses, dogs and cattle in Cordoba, Colombia. In this study, 1.105 ticks were removed from 226 zebu cattle (Bos indicus), 87 dogs (Canis lupus familiaris) and 19 horses (Equus caballus), from different localities of Cordoba. Ticks were identified taxonomically and PCR assays were used for the amplification of Anaplasma sp. and Ehrlichia sp. DNA. The amplification products were sequenced and analyzed. From the 1,105 ticks examined, 679 (61.5%) were Rhipicephalus microplus, collected from cattle, 353 (32%) were Rhipicephalus sanguineus from dogs and 73 (6,6%) Dermacentor nitens collected on horses; 332 pools were formed to develop the PCR assay. Anaplasma sp. and Ehrlichia sp. DNA was detected in 5.7% (19/332 pools). Direct sequencing of amplicons showed that seven sequences had similarities between 99–100% with Anaplasma marginale, one sequence showed 100% identical with Anaplasma phagocytophilum, seven sequences showed 100% identity with Ehrlichia ewingii, one sequence had 100% identity with E. chaffensis and three sequences showed similarities of 99% and 95% with Ehrlichia mineirensis and Ehrlichia canis respectively. In conclusion, several tick-borne pathogens identified in this survey suggests that there is a risk for the emergence of tick-borne diseases in domestic animals and humans in Colombia. Our data provides evidence of Ehrlichia and Anaplasma species circulating in ticks from Cordoba.