Allelic frequency is one of the important concepts in bioinformatics and its mathematical modeling information and statistical distribution has great importance in the detection of genetic mutations or disorder in future generations. The interesting point regarding the allelic frequencies is that they have random variations and as a consequence, follow a certain statistical distribution. So far, many studies have been carried out about the estimation of allelic frequencies. Especially, Martinez et al. (2015) and Martinez et al. (2017) worked on the estimation of allelic frequency by considering the Hardley-Weinberg equilibrium, a multinomial distribution for genotypes, and a beta distribution for allelic random variations. Karimnezhad and Moradi worked on the allelic frequency estimation using a robust Bayesian approach in 2018 as well. In the present article, we work on the Bayesian allelic frequency estimation under various loss functions and we deal with an optimal decision-making problem using a simulation study. To this end, we compare the performance of the derived estimators using risk and absolute value of bias criteria.