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Rickettsial pathogens are among the emerging and re-emerging vector-borne zoonoses of public health importance. Reports indicate human exposure to Rickettsial pathogens in Namibia through serological surveys, but there is a lack of data on infection rates in tick vectors, hindering the assessment of the relative risk to humans. Our study sought to screen Ixodid ticks collected from livestock for the presence of <i>Rickettsia</i> species in order to determine infection rates in ticks and to determine the <i>Rickettsia</i> species circulating in the country. We collected and pooled <i>Hyalomma</i> and <i>Rhipicephalus</i> ticks from two adjacent regions of Namibia (Khomas and Otjozondjupa) and observed an overall minimum <i>Rickettsia</i> infection rate of 8.6% (26/304), with an estimated overall pooled prevalence of 9.94% (95% CI: 6.5–14.3). There were no statistically significant differences in the estimated pooled prevalence between the two regions or tick genera. Based on the nucleotide sequence similarity and phylogenetic analysis of the outer membrane protein A (n = 9) and citrate synthase (n = 12) genes, BLAST analysis revealed similarity between <i>Rickettsia africae</i> (n = 2) and <i>Rickettsia aeschlimannii</i> (n = 11), with sequence identities ranging from 98.46 to 100%. Our initial study in Namibia indicates that both zoonotic <i>R. africae</i> and <i>R. aeschlimannii</i> are in circulation in the country, with <i>R. aeschlimannii</i> being the predominant species.