The R package PopGenome is a population genomics package used in R software for the analysis of genome data. It can efficiently process both genome-scale data and large sets of individual loci. PopGenome reads DNA alignments and single-nucleotide polymorphism (SNP) data sets in generally common formats which are simpler. The package offers a wide range of diverse population genetics analyses which includes neutrality tests, population differentiation and linkage disequilibrium. The integration in R helps in effortless analysis and production of publication quality.