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Arthropod vectors transmit a diversity of animal and human pathogens, ranging from RNA viruses to protozoal parasites. Chemotherapeutic control of pathogens has classically focused either on insecticides that kill the vector itself or antimicrobials for infected patients. The limitation of the former is that it targets both infected and uninfected vectors and selects for resistant populations while the latter requires prompt and accurate diagnosis. An alternative strategy is to target vector molecules that permit the pathogen to establish itself, replicate, and/or develop within the vector. Using the rickettsial pathogen Anaplasma marginale and its tropical tick vector, Rhipicephalus microplus, as a model, we tested whether silencing specific gene targets would affect tick infection rates (the % of fed ticks that are infected with the pathogen) and pathogen levels within infected ticks. Silencing of three R. microplus genes, CK187220, CV437619 and TC18492, significantly decreased the A. marginale infection rate in salivary glands, whereas gene silencing of TC22382, TC17129 and TC16059 significantly increased the infection rate in salivary glands. However in all cases of significant difference in the infection rate, the pathogen levels in the ticks that did become infected, were not significantly different. These results are consistent with the targeted genes affecting the pathogen at early steps in infection of the vector rather than in replication efficiency. Identifying vector genes and subsequent determination of the encoded functions are initial steps in discovery of new targets for inhibiting pathogen development and subsequent transmission.