Background Ticks are important vectors of many pathogens that have contributed to the morbidity and mortality of humans and domestic animals worldwide. Wildlife species have also been implicated as reservoir hosts of a variety of tick-borne pathogens. The objective of this study was to determine which tick-transmitted pathogens were present in the animals harvested from the forest in Trinidad for human consumption. Methods Thin blood smears from 43 neotropical animals were examined microscopically for tick-borne pathogens. Additionally, DNA extraction and PCR amplification of the 16S rRNA gene were used for amplification of Anaplasma and Ehrlichia while the gltA gene was used for Bartonella, and Rickettsia spp. and the 18S rRNA gene for Babesia, Hepatozoon and Theileria species. Results Pathogen DNA was amplified from four samples (a deer, collared peccary and two agoutis). Sequencing of the amplified products from the deer and collared peccary revealed 99.8% homology to Anaplasma bovis and 98.8% homology to Ehrlichia canis, respectively. Sequences from two agoutis revealed 90.4% homology to Theileria spp. DNA of Hepatozoon spp., Bartonella spp. Babesia spp. and Rickettsia spp. was not detected in any of the screened samples. An incidental finding in this study was the presence of bacteria in the blood of animals. Conclusions The results indicate that the DNA of tick-transmitted pathogens is present at a frequency of about 10% in the study population and suggests that neotropical mammals may serve as a source for the potential transmission of tick-borne pathogens to domestic animals and humans. In addition, physicians and hunters should be aware of the symptoms associated with zoonotic tick-borne pathogens so that these infections can be recognised, diagnosed and treated promptly. Bacteria present in carcasses can pose a food safety hazard and hunters should be trained in proper harvesting and handling of carcasses. Graphical Abstract