Molecular epidemiology refers to the use of molecular tools in assessing the status of a cycle of a disease in a specific population. Currently, easy, fast, and high performance molecular tools are widely used in identifying parasites in clinical and biological samples. The aim of this study was to review molecular tools for better understanding of parasitic infection in taxonomic and epidemiological studies. Many researches have provided a variety of methods and markers for identification and evaluation of genetic diversity and elimination of taxonomic problems, especially at the level of species or subspecies of various parasites. Many of these studies are on the prevalence of concurrent infections with different species and subtypes or strains of a parasite. So far, different pieces of rDNA, mtDNA, and kDNA have been used for identification and phylogenetic analysis. If the purpose of a study is to determine intra-specific variations of the parasite, it is better to use sequencing ribosomal ITS1 and mitochondrial CO1. In addition, SSU rDNA and LSU rDNA are used in phylogenetic analysis and taxonomy. It can be concluded that new molecular tools and markers are good alternatives to traditional methods because in many endemic areas successful treatment depends on rapid and accurate diagnosis.