Canine babesiosis and canine ehrlichiosis is important tick-borne diseases of dogs that pose major health problem worldwide especially in tropics and sub-tropics. In our study, a total of 450 blood samples from farm dogs of three different ecological zones of the Punjab province of Pakistan, were examined by using microscopy and PCR. Examination of thin blood smears revealed an overall prevalence of 12.8 % (58/450) of canine babesiosis. However, molecular technique revealed 46.8 % (211/450) samples positive for B. gibsoni as confirmed by the amplification of 671 bp of 18S rRNA gene of B. gibsoni while 7.3 % (33/450) samples were positive for B. vogeli as it was confirmed by the amplification of 590 bp amplicon. Similarly, 45.5 % (205/450) were found positive for E. canis through PCR as it was confirmed through the amplification of 389 bp of 16S RNA amplicon. The highest prevalence of E. canis, B. gibsoni and B. vogeli was found in district Kasur as 60 %, 56.5 % and 10.6 % followed by district Rawalpindi as 32.6 %, 42.6 % and 6.0 % and district Muzaffargarh as 44.0 %, 40.6 % and 5.3 % respectively. The prevalence of coinfection was also identified in all three districts. The highest prevalence of E. canis and B. gibsoni was found in district Kasur 78.7 % followed by district Muzaffargarh 73.3 % and district Rawalpindi 66.6 %, respectively. The highest prevalence of E. canis and B. vogeli was found in district Rawalpindi 16.6 % followed by district Kasur 14.8 % and district Muzaffargarh 10.5 %. Similarly, coinfection of B. gibsoni and B. vogeli was also detected and the highest prevalence was found in district Rawalpindi 11.1 % followed by district Muzaffargarh 10.5 % and district Kasur 3.1 %. However, the coinfection of E. canis, B. gibsoni and B. vogeli was found higher in district Kasur 6.6%, followed by district Rawalpindi 5.5 % and district Muzaffargarh 5.3 %, respectively. The alignment of nucleotide sequence of B. gibsoni showed that there was transition and polymorphism at two points (351 and 574). The alignment of E. canis showed that only one haplotype had transition at two points (339 and 342), while the alignment of B. vogeli showed great genetic variation in their alignment. There were transition and polymorphism at ten different position of B. vogeli sequence alignment. The phylogenetic analysis of B. gibsoni revealed that all of our haplotypes were making the single group with previously reported sequences from world except one haplotype that was making an alone group. Similarly, the phylogenetic analysis of E. canis revealed that all of our haplotypes were making two clades. One clade consists of 14 of our haplotype with other reported sequences, while second clade only consists of our single haplotype ECAN 3, while the phylogenetic analysis of B. vogeli showed that all of our three haplotypes were making three clades due to high genetic variability with previously reported sequences from world. The results of multivariate analysis showed that the prevalence of canine babesiosis is associated with various risk factors. The prevalence of canine babesiosis is higher in central Punjab and younger age of the dogs, while breed and sex of the host were not significantly associated with the prevalence of the diseases. When we were analyzing our samples for hemoparasites of dogs, we also found Hepatozoon canis which is also one of the important tick-borne pathogens of canines and is distributed worldwide. However, very little information of this parasite is available from Pakistan. This project provides the first genetic characterization of H. canis from farm dogs of three agroecological zones of Punjab, Pakistan. A conventional PCR targeting 18S rRNA gene was used to characterize H. canis from farm dogs from three districts, including Kasur, Rawalpindi and Muzaffargarh in Punjab. Of 341 blood samples tested, 155 (45.5 %) were positive for H. canis, including 73 samples (61.3 %) from Kasur, 46 samples (42.5 %) from Rawalpindi and 36 (31.5 %) from Muzaffargarh. Phylogenetic analyses revealed that 18S rRNA sequences of H. canis from this study clustered in three clades with those of H. canis from previously published studies, though with low statistical support. This study provides the first insight into H. canis from farm dogs in Pakistan as well as lays a foundation for future studies of the parasite in various agro-ecological zones to assess the impact of canine hepatozoonosis in Pakistan where the pet ownership of dogs is increasing.