Leucocytozoon sabrazesiis an intracellular haemoprotozoan parasite responsible for leucocytozoonosis, which is transmitted by insect vectors and affects chickens in tropical and subtropical areas in many countries. It causes huge economic losses due to decreased meat and egg production. In the present study, we used nested PCR to determine the genetic diversity of L. sabrazesibased on the cytb, coxI, coxIIIand concatenated genes in chickens in Thailand. In addition, we found co-infections between L. sabrazesiand Plasmodiumspp. (P. gallinaceumor P. juxtanucleare) in chickens that were not identified by microscopic examination of blood smears. The phylogenetic analysis indicated that L. sabrazesi cytband coxIIIgenes were conserved with similarity ranging from 99.9 to 100% and 98 to 100%, respectively whereas the coxIgene was diverse, with similarities ranging from 97 to 100%. These findings ascertained the nucleotide analysis of the cytb, coxI, coxIIIand concatenated sequences in which 4, 8, 10 and 9 haplotypes were found, respectively. In addition, it was found that the large number of synonymous substitutions and conservative amino acid replacements in these mitochondrial genes occurred by non-synonymous substitution. The evolutionary analysis of the Ka/Ksratio supported purifying selection and the negative values of both Fu’s Fs and Tajima’s Dindicate selective sweep especially for the coxIgene. The entropy and Simplot analysis showed that the genetic variation in populations of Plasmodiumspp. was higher than in Leucocytozoon.Hence, the nucleotide sequences of three mitochondrial genes could reflect the evolutionary analysis and geographic distribution of this protozoan population that switches hosts during its life cycle.