Haemogregarines (Apicomplexa: Adeleorina) are the most common and widespread reptilian blood parasites. Haemogregarina stepanowi was the first haemogregarine described from a reptile, the European pond turtle Emys orbicularis, and initial assessments indicated it was widespread across different pond turtle host species across much of Europe, the Middle East and North Africa. However, recent molecular assessments have indicated the presence of multiple genetically distinct forms in North Africa and the Iberian Peninsula, and extensive mixed infections which may be associated with a negative impact on the hosts. Here, we screened two native species, E. orbicularis and Mauremys rivulata, and the introduced Trachemys scripta from Serbia and North Macedonia for haemogregarines by amplifying and sequencing part of the 18S rRNA gene of these parasites, and used a standard DNA barcoding approach to identify leeches, the final host, attached to pond turtles. Our results again demonstrate the occurrence of considerable diversity of parasites in the analysed pond turtle species, and that T. scripta are likely infected by local haemogregarine parasites, and not those that are found in its native range. Leeches were identified as Placobdella costata, part of a lineage from Northern Europe. Mixed infections within pond turtles were again common. Current haemogregarine taxonomy does not reflect the genetic diversity identified, and a full taxonomic reassessment is needed.