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Tick-borne pathogens (TBPs) pose a significant threat to livestock, including bovine species. This study aimed to investigate TBPs in cattle and ticks across four sampling points, utilizing real-time microfluidic PCR. The results revealed that <i>Rhipicephalus microplus</i> ticks were found infesting all animals. Among the detected TBPs in cattle, <i>Anaplasma marginale</i> was the most frequently identified, often as a single infection, although mixed infections involving <i>Rickettsia felis</i>, uncharacterized <i>Rickettsia</i> sp., and <i>Anaplasma</i> sp. were also observed. In ticks, <i>A. marginale</i> was predominant, along with <i>R. felis</i>, <i>Rickettsia</i> sp., and <i>Ehrlichia</i> sp. It is noteworthy that although <i>A. marginale</i> consistently infected all cattle during various sampling times, this pathogen was not detected in all ticks. This suggests a complex dynamic of pathogen acquisition by ticks. A phylogenetic analysis focused on the identification of <i>Anaplasma</i> species using amplified 16S rDNA gene fragments revealed the presence of <i>A. marginale</i> and <i>Anaplasma platys</i> strains in bovines. These findings underscore the presence of multiple TBPs in both cattle and ticks, with <i>A. marginale</i> being the most prevalent. Understanding the dynamics and phylogenetics of TBPs is crucial for developing effective control strategies to mitigate tick-borne diseases in livestock.