Ticks are vectors of several microorganisms responsible for infectious diseases in human and animals, such as <i>Anaplasma phagocytophilum</i> and <i>Coxiella burnetii.</i> In this study, we investigated the prevalence of these two bacteria in 62 889 <i>Ixodes ricinus</i> ticks in selected regions covering all Switzerland. A high prevalence of 11.9% of <i>A. phagocytophilum</i> DNA was observed by real-time PCR on 8534 pools of ticks. This pool prevalence corresponds to an estimated prevalence of 1.71% in individual tick. A total of 144 of the 171 collection sites (84.2%) were positive for the presence of <i>A. phagocytophilum,</i> and these sites were homogenously distributed throughout Switzerland. Such prevalence and geographical distribution underline the risk of human and animal exposure to <i>A. phagocytophilum</i> and highlight the need to assess the epidemiology and clinical diagnosis of human and animal anaplasmosis in Switzerland. However, DNA of <i>C. burnetii</i> was never found in any tick pool. This absence suggests a very low role of <i>I. ricinus</i> ticks as vector and reservoir of <i>C. burnetii</i> in Switzerland, and it supports previous reports demonstrating the role of sheep and goats in the epidemiology of Q fever. However, considering its pathogenic potential, it is necessary to keep monitoring for the possible reemergence of this bacterium in ticks in the future.