Coxiella species are known to be potentially pathogenic tickborne organisms. This study was aimed to investigate the presence of Coxiella sp. in Rhipicephalus sanguineus ticks in Cebu, Philippines by molecular based techniques. A total of 164 ticks were collected from 36 dogs and analyzed by a Nested Polymerase Chain Reaction (PCR) for the amplification of partial 16S ribosomal RNA gene region. Nine ticks (5.5%) obtained from 5 dogs were found positive. Sequencing revealed partial DNA fragments of Coxiella spp. which were 96.3% and 98.1-100% identical to Coxiella burnetii and Coxiella sp. endosymbiont, respectively. The detected DNA fragments also shared 98.3-100% identities with each other. This study is the first report on the existence of Coxiella spp. from Rhipicephalus sanguineus ticks in Cebu, Philippines.