The aim of the present study was to conduct multiplex PCR for detection of two haemotropic Mycoplasma species in dogs from central Iran and study their relationship with epidemiological factors. In order to achieve this, blood samples from 100 Esfahan dogs were analysed by PCR to evaluate haemoplasma infection status. Thirteen were infected with an organism closely related to Mycoplasma haemocanis, and ten were infected with Candidatus Mycoplasma haematoparvum, whilst three dogs were contaminated with both organisms. The results showed a significant difference between young (1–5 years old) and ectoparasite-infected dogs for the presence of haemotropic Mycoplasma. Our survey indicates that multiplex PCR assay is able to successfully detect haemotropic Mycoplasma in dogs.