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Background  Only limited information is currently available on the prevalence of vector borne and zoonotic pathogens in dogs and ticks in Nigeria. The aim of this study was to use molecular techniques to detect and characterize vector borne pathogens in dogs and ticks from Nigeria.    Methodology/Principal Findings  Blood samples and ticks ( Rhipicephalus sanguineus ,  Rhipicephalus turanicus  and  Heamaphysalis leachi ) collected from 181 dogs from Nigeria were molecularly screened for human and animal vector-borne pathogens by PCR and sequencing. DNA of  Hepatozoon canis  (41.4%),  Ehrlichia canis  (12.7%),  Rickettsia  spp. (8.8%),  Babesia rossi  (6.6%),  Anaplasma platys  (6.6%),  Babesia vogeli  (0.6%) and  Theileria  sp. (0.6%) was detected in the blood samples. DNA of  E. canis  (23.7%),  H. canis  (21.1%),  Rickettsia  spp. (10.5%),  Candidatus  Neoehrlichia mikurensis (5.3%) and  A. platys  (1.9%) was detected in 258 ticks collected from 42 of the 181 dogs. Co- infections with two pathogens were present in 37% of the dogs examined and one dog was co-infected with 3 pathogens. DNA of  Rickettsia conorii israelensis  was detected in one dog and  Rhipicephalus sanguineus  tick. DNA of another human pathogen,  Candidatus  N. mikurensis was detected in  Rhipicephalus sanguineus  and  Heamaphysalis leachi  ticks, and is the first description of  Candidatus  N. mikurensis in Africa. The  Theileria  sp. DNA detected in a local dog in this study had 98% sequence identity to  Theileria ovis  from sheep.    Conclusions/Significance  The results of this study indicate that human and animal pathogens are abundant in dogs and their ticks in Nigeria and portray the potential high risk of human exposure to infection with these agents.

Molecular Detection and Characterization of Tick-borne Pathogens in Dogs and Ticks from Nigeria