Rickettsioses caused by Rickettsia felis are an emergent global threat. Historically, the northern region of the province of Caldas in Colombia has reported murine typhus cases, and recently, serological studies confirmed high seroprevalence for both R. felis and R. typhi. In the present study, fleas from seven municipalities were collected from dogs, cats, and mice. DNA was extracted and amplified by polymerase chain reaction (PCR) to identify gltA, ompB, and 17kD genes. Positive samples were sequenced to identify the species of Rickettsia. Of 1,341 fleas, Ctenocephalides felis was the most prevalent (76.7%). Positive PCR results in the three genes were evidenced in C. felis (minimum infection rates; 5.3%), C. canis (9.2%), and Pulex irritans (10.0%). Basic Local Alignment Search Tool (BLAST) analyses of sequences showed high identity values (> 98%) with R. felis, and all were highly related by phylogenetic analyses. This work shows the first detection of R. felis in fleas collected from animals in Colombia.