Microsatellite markers historically have been one of the most popular tools for assessing the genetic diversity of livestock due to their nature and polymorphism with their motifs. A challenging problem that arises in this domain is the occurrence of errors in the genotyping process. Additionally, errors in genotyping and allele size determination occur when the genotype determined by the molecular technique does not match the actual genotype in the individual's genome. Furthermore, errors have a direct impact on the ability to differentiate between individuals in a population, and incorrect conclusions and mislead breeders in decisions. With this motivation, the present report aims to evaluate the efficiency of the pig-tailing technique on the parameters of molecular differentiation based on microsatellites in a population of camels. For this purpose, a total of 20 unrelated camel individuals from different regions of Yazd province were collected, and then genomic DNA was extracted using routine salting out methods. Then, five microsatellite polymorphic sites were selected according to Food and Agriculture Organization (FAO), and two groups of common primers and pig-tailed primers (GTTTCTT nucleotide sequence added to 5' reverse primer) were fluorescently candidates for in-population differentiation and diversity. Clustering and principal component analysis (PCA) was performed using the R Package (version 4.2.0), MEGA, and PRCOMP package under the R environment. Interestingly, the results of genotyping showed that the pig-tailing technique tends to reduce the false band patterns (stutter) and also significantly reduce the chance of error in di-motif microsatellite type. On this basis, we can conclude that the pig-tailing strategy in microsatellite genotyping in camel’s genetic diversity, seems to be a suitable method.