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Simple Summary: Tick-transmitted diseases are the main constraint in the development of the livestock industry in Tanzania. In this study, we investigated the occurrence of pathogens transmitted by ticks in local breeds of cattle kept under a free-range management system in the Tanga region, Tanzania. The study revealed a high infection rate of the pathogens that cause theileriosis (Theileria parva, Theileria mutans and Theileria taurotragi), anaplasmosis (Anaplasma marginale) and babesiosis (Babesia bigemina) in the sampled cattle. Moreover, the results show that a good number of cattle were infected with more than one pathogen. Notably, the study revealed different strains of Babesia bigemina and Theileria mutans in the population of cattle involved in the study. Furthermore, similar strains of Theileria parva and Anaplasma marginale were revealed. The information produced by this study will help policy makers to set up control strategies to contain these diseases. The control of tick-transmitted diseases will certainly improve cattle health and production. Therefore, the livelihood of the pastoralists of the Tanga region in Tanzania will be improved. Tick-borne diseases (TBDs) are a major hindrance to livestock production in pastoral communities of Africa. Although information on tick-borne infections is necessary for setting up control measures, this information is limited in the pastoral communities of Tanzania. Therefore, this study aimed to provide an overview of the tick-borne infections in the indigenous cattle of Tanzania. A total of 250 blood samples were collected from the indigenous zebu cattle in the Tanga region, Tanzania. Then, we conducted a molecular survey using the polymerase chain reaction (PCR) and gene sequencing to detect and identify the selected tick-borne pathogens. The PCR was conducted using assays, based on Theileria spp. (18S rRNA), Theileria parva (p104), Theileria mutans and T. taurotragi (V4 region of the 18S rRNA), Babesia bigemina (RAP-1a), B. bovis (SBP-2), Anaplasma marginale (heat shock protein groEL) and Ehrlichia ruminantium (pCS20). The PCR screening revealed an overall infection rate of (120/250, 48%) for T. mutans, (64/250, 25.6%) for T. parva, (52/250, 20.8%) for T. taurotragi, (33/250, 13.2%) for B. bigemina and (81/250, 32.4%) for A. marginale. Co-infections of up to four pathogens were revealed in 44.8% of the cattle samples. A sequence analysis indicated that T. parva p104 and A. marginale groEL genes were conserved among the sampled animals with sequence identity values of 98.92–100% and 99.88–100%, respectively. Moreover, the B. bigemina RAP-1a gene and the V4 region of the 18S rRNA of T. mutans genes were diverse among the sampled cattle, indicating the sequence identity values of 99.27–100% and 22.45–60.77%, respectively. The phylogenetic analyses revealed that the T. parva (p104) and A. marginale (groEL) gene sequences of this study were clustered in the same clade. In contrast, the B. bigemina (RAP-1a) and the T. mutans V4 region of the 18S rRNA gene sequences appeared in the different clades. This study provides important basement data for understanding the epidemiology of tick-borne diseases and will serve as a scientific basis for planning future control strategies in the study area. [ABSTRACT FROM AUTHOR]