Mexico is one of the top 10 biodiverse countries in the world, with approximately 800 species of reptiles, more than half of which are endemic. Biodiverse regions tend to also have rich parasite communities, but these are often poorly known relative to their hosts. In this study, we focused on the presence of blood parasites of the genus Hepatozoon in wild-caught squamate reptiles from Mexico, employing both microscopic and molecular detection methods. A total of 298 individual squamates representing 12 families, 25 genera, and 38 species were collected during field expeditions. Gamonts of Hepatozoon spp. were detected by microscopic observation of blood smears in 38 of 295 individuals belonging to 6 families (12.9% prevalence). PCR variants of 18S rRNA of the Hepatozoon spp. from eight squamate individuals were included in phylogenetic analyses; five species of iguanids (two individuals of Ctenosaura pectinata, and one individual of Ctenosaura acanthura, Crotaphytus dickersonae, Iguana iguana, and Sauromalus ater), one helodermatid specimen (Heloderma horridum) and one colubrid specimen (Pituophis deppei). Phylogenetic analyses (Bayesian inference and maximum likelihood) revealed the existence of seven variants of the Hepatozoon parasites belonging to six main lineages, as well as showing that Hepatozoon lineages vary between hosts. In conclusion, our data represents a pilot study concerning the presence of Hepatozoon parasites in various reptile hosts from different geographical regions in Mexico.