Many stress-related interactions such as pathogen infection, insect tolerance, salt tolerance, auxin degradation, cell wall lignification, tissue suberization, and plant senescence involve various isoforms of peroxidases. Peroxidase gene polymorphism (POGP) markers have been used to estimate diversity, relationships and population structure among 80 Citrus and their relatives in Aurantioideae by using unweighted pair group method arithmetic average (UPGMA) and bayesian substructuring analysis. Fourteen primers produced a total of 148 fragments and 147 of them were polymorphic. The UPGMA analysis demonstrated that the accessions had a similarity range from 0.27 to 0.98 and were distinguished. The results of this study were mostly consistent with previous reports of different marker systems, but few different findings were also detected. The subtribe Clauseninae (tribe Clauseneae) did not clearly separate from the subtribes of the tribe Citreae. Substructuring analysis indicated that there were six subpopulations among the accessions studied. This study revealed that the POGP markers can be utilized to estimate genetic diversity, relationships and population structure in Citrus and related species in the Aurantioideae subfamily.