The study aimed at determining the prevalence of Babesia species infection in dogs in the Federal Capital Territory, Abuja, Nigeria and identification of ticks of the sampled animals. It further evaluated the parasitological and molecular characteristics of the ticks and Babesia species. A total of 480 asymptomatic dogs were sampled for tick and blood, using standard method. Ticks collected were identified to generic level using morphological features in a dissecting microscope. Thick and thin blood smears were prepared, Geimsa stained and examined microscopically, for intra-erythrocytic merozoites of Babesia spp. Haematological parameters of sampled dogs were evaluated using automated haematology analyser. Genomic DNA was extracted from 30 Rhipicephalus spp. of ticks and 15 B. canis positive whole blood, followed by partial amplification of 18S rRNA gene using genus specific primers. The PCR products were purified and sequenced. The chromatograms were trimmed in ApE software, and aligned to generate a consensus sequence for each isolate. The nucleotide sequence BLAST analysis was carried out in NCBI database. Correct sequences of 9R. sanguineus and 3B. c. vogeli were obtained and deposited in the GenBank using Bank it tool.Multiple sequence alignments was carried out using ClustralW in MEGA7.0 software. Phylogenetic trees were constructed for Rhipicephalus and Babesia species using neighbour-joining and maximum likelihood methods respectively. The results showed an overall prevalence of 10.8% and 3.1% B. canis infection in dogs for thick and thin smears techniques respectively. The prevalence of Babesia infection in FCT based on sampled location was highest (12.5%) in Gwagwalada,Abuja Municipal and Kwali Area Councils and lowest (6.3%) in Abaji Area Council. The prevalence of B.canis infection based on sex showed that males had a higher (13.7%) than the females with 8.3% infection rate. The prevalence based on breed showed that exotic breeds had the highest (12.9%) while the cross breed had the lowest of 9.4% B. canis infection rate The prevalence based on purpose showed that hunting dogs had the highest (11.3%) while the pet dogs recorded no Babesiaspp. infections. The prevalence based on season showed that the rainy season had higher (14.6%) than the dry season with 7.1% of B. canis infection. The prevalence of Babesia infection based on tick infestations showed that tick infested dogs had higher (17.1%) than dogs without ticks, with 3.5% infection rate. The percentage of tick attachment based on predilection sites showed that the ear region had the highest (45%), while the scrotal and the mammary region had the lowest with 4.0%. There was significant (p < 0.05) association between rate of Babesia infection and age group, purpose, season and tick infestation. No significant association was observed between Babesia infection and sex, breed, and sampled locations. The haematological parameters showed higher values for packed cell volume, haemoglobin concentration, red blood cell count and platelets in Babesia negative dogs.However,red blood cell count, lymphocytes and monocytes values were lower when compared with Babesia positive dogs. Out of the 2,043 ticks collected from sampled dogs, 99.9% were Rhipicephalus spp. and 0.1% were Amblyomma spp. The PCR amplified at 173bp and 612bp gene segments on gel electrophorogram for Rhipicephalus spp. and B. canis respectively. The BLAST analysis showed 96-100% and 100% similarity with R. sanguineus and B. c. vogeli respectively in the GenBank. The phylogenetic trees showed that sequences of R. sanguineus isolates from the study area(accession numbers: KY 799078 – KY799086) clustered together while the sequences of B. c. vogeli isolates (accession numbers: MF000388, MF000389, MF000390), separated into two different clades. The study concludes that R. sanguineus was the common ticks infesting dogs and B. canis vogeli was the subspecies of B. canis infecting the sampled dogs in the study area.