Despite of having rich reptilian fauna, the wild lizards from Pakistan remained unexplored for the presence of blood borne parasites. The present study was designed to report the molecular epidemiology and phylogenetic evaluation of various blood borne pathogens (Hepatozoon sp., Schellackia spp., Toxoplasma gondii, Plasmodium spp., Haemoproteus spp. and Leucocytozoon spp.) in blood samples of wild lizards (N = 84), trapped during March 2022 till June 2023 from district Karak and Dir in Khyber Pakhtunkhwa (Pakistan). Seven lizard species were identified during present study. Our results revealed that 11 out of 84 (13%) lizards were Haemogregarines infected. Infected lizards included Laudakia (L.) tuberculata (1/4, 25% prevalence), L. pakistanica (3/15, 20%) and L. agrorensis (7/53, 13%). DNA sequencing and BLAST analysis confirmed the presence of Hepatozoon sp. and Lankesterella sp. While the lizards were negative for the remaining screened pathogens. Phylogenetic analysis of both pathogens revealed genetic diversity among the Pakistani isolates and they clustered with isolates detected in reptiles, birds and rodents from different countries. For L. tuberculata, Haemogregarines prevalence significantly varied between the sample collection sites. In conclusion, this is the first report from Pakistan documenting a relatively higher Haemogregarines infection rate in wild Pakistani lizards. Further, comprehensive and large-scale studies must be conducted in unexplored geo-climatic regions of Pakistan to report the actual prevalence of Haemogregarines among the wild lizards as well as in other wildlife species. These findings will add to our knowledge regarding the genetic diversity and the interactions of these parasites with their hosts that will lead towards parasite control.