BackgroundVector-/tick-borne pathogens (V/TBPs) pose a potential threat to human and animal health globally. Information regarding canine V/TBPs is scarce and no specific study has been conducted so far to explore the microbial diversity within ticks infesting dogs from Pakistan. Herein, this knowledge gap is addressed by assessing the genetic diversity and prevalence pattern of V/TBPs in ixodid ticks with special implications for public and canine health.MethodsA total of 1150 hard ticks were collected from 300 dogs across central Khyber Pakhtunkhwa (KP), Pakistan. After morpho-molecular identification, 120 tick samples were screened for the presence of V/TBPs by amplifying16S rRNA/gltA(Rickettsia/EhrlichiaandWolbachiasp.),18S rRNA(Theileriasp.) andcox1(Dirofilariasp.) genes through PCR followed by sequencing and phylogenetic study.ResultsIn toto, 50 ixodid ticks (50/120, 41.7%) were found positive for V/TBPs DNA. The detected V/TBPs were categorized into five genera and eight species, viz.Ehrlichia(E. canisandEhrlichiasp.),Rickettsia(R. massiliae, R. raoultiiandRickettsiasp.),Theileria(T. annulata),Dirofilaria(D. immitis) andWolbachia(Wolbachiasp.). The pathogen prevalence patterns showed thatR. massiliaewas the most prevalent zoonotic V/TBP (19.5%), followed byE. canis(10.8%),Rickettsiasp. (7.5%), R. raoultii(6.7%),T. annulata(5.8%),D. immitis(5.8%),Wolbachiasp. (4.2%) andEhrlichiasp. (3.3%), respectively. Among the screened tick species, mostRhipicephalus sanguineussensu lato samples were found positive for V/TBP DNA (20/20,100%) followed byRh. turanicussensu stricto (13/20, 65%),Hyalomma dromedarii(8/20, 40%),Rh. haemaphysaloides(6/20, 30%),Hy. excavatum(2/20, 10%) andRh. microplus(1/20, 5%). Co-occurrence of V/TBP was also detected in tick specimens (single V/TBP infection: 32 ticks; double and triple: 13 and 5 tick samples). The detected pathogens shared a phylogenetic relationship with similar isolates published in NCBI GenBank from Old and New World countries.ConclusionIxodid ticks infesting dogs harbor a diverse array of V/TBPs including zoonotic agents from Pakistan. Furthermore, the presence ofD. immitisin ticks that infest dogs raises the possibility that this parasite has either attained its dead-end host (i.e. the tick) while feeding on dogs or has expanded its range of intermediate/paratenic hosts. Further research work is needed to investigate the epidemiology and confirm the vector competence of screened tick species for these pathogens from Pakistan.Graphical AbstractSupplementary InformationThe online version contains supplementary material available at 10.1186/s13071-023-05804-2.