Background: Bacteria from the genus Rickettsia are causative agents of arthropod-borne zoonotic diseases including spotted fevers as well as epidemic and endemic typhus. Different species of Fleas could act as reservoir and vectors of two pathogenic Rickettsia species, R. typhi and R. felis. A considerable number of cases of flea-borne typhus have been reported in Caldas State from the past years and recently we have confirmed 46% and 50% of seroprevalence for R. typhi and R. felis, respectively and two clinical infections with the latter. Until now, there are no reports of vectors of these Rickettsia species in this region. The aim of this work was identify by molecular techniques Rickettsia species in fleas collected in seven municipalities from Caldas State, Colombia. Methods: A total of 1341 fleas were collected from dogs, cats, rats and mice, between 2010 and 2011 from seven municipalities in the north region of Caldas State. All specimens were identified by taxonomy keys and conserved in ethanol for processing. Pools of these fleas were constituted by origin, host and flea species, and submitted to DNA extraction with a commercial kit. All samples were initially screened for gltA gene by PCR with the primers CS-78/CS-323 and positive samples were further analysed for ompB and htrA (17kD) genes with the pair of primers 120-M59/120-807 and 17kD1/17kD2, respectively. Results: From the 1341 fleas collected, Ctenocephalides felis were the most common species in six Municipalities (76.7%). Other species obtained were C. canis, Pulex irritans and Xenopsylla cheopis. Neira was the municipality with the highest proportion of fleas with 395 specimens (29.5%). From these samples, 182 pools were constituted and from these, 124 were positive for gltA (68%), 104 for ompB (57%), 91 for htrA and 79 for the three genes (43%). Conclusion: These results confirm the high circulation of bacteria from the genus Rickettsia in fleas collected principally in dogs and cats from municipalities with confirmed clinical cases of Flea-borne Rickettsiosis. PCR products are in process of sequencing for further species identification.