The R package pegas is designed for population genetic data analysis, integrating with existing R packages ape and adegenet. It provides functions for standard population genetic methods and allows for the development of new methods. The package uses R's flexible data structures for efficient data handling. The 'loci' class is a data frame where rows represent individuals and columns represent loci, enabling efficient computation of genotypic and allelic frequencies. The 'haplotype' class extends the 'DNAbin' class from ape, allowing for the identification of individuals within haplotypes. pegas handles missing data explicitly and supports various population genetic analyses, including Hardy–Weinberg equilibrium, FST, molecular variance analysis, haplotype networks, and Tajima's D. It also includes functions for reading and writing data files and for manipulating data structures. The package is distributed through CRAN and includes a tutorial for data input. pegas uses R's graphical capabilities for visualizing data, such as haplotype networks. The integrated-modular approach of pegas complements the functionalities of adegenet, ape, and pegas, providing tools for spatial and multivariate analyses, tree structures, DNA sequence manipulation, and basic population genetic analyses. The package is designed to be used independently or in combination with other packages, offering a flexible and efficient solution for population genetic data analysis.The R package pegas is designed for population genetic data analysis, integrating with existing R packages ape and adegenet. It provides functions for standard population genetic methods and allows for the development of new methods. The package uses R's flexible data structures for efficient data handling. The 'loci' class is a data frame where rows represent individuals and columns represent loci, enabling efficient computation of genotypic and allelic frequencies. The 'haplotype' class extends the 'DNAbin' class from ape, allowing for the identification of individuals within haplotypes. pegas handles missing data explicitly and supports various population genetic analyses, including Hardy–Weinberg equilibrium, FST, molecular variance analysis, haplotype networks, and Tajima's D. It also includes functions for reading and writing data files and for manipulating data structures. The package is distributed through CRAN and includes a tutorial for data input. pegas uses R's graphical capabilities for visualizing data, such as haplotype networks. The integrated-modular approach of pegas complements the functionalities of adegenet, ape, and pegas, providing tools for spatial and multivariate analyses, tree structures, DNA sequence manipulation, and basic population genetic analyses. The package is designed to be used independently or in combination with other packages, offering a flexible and efficient solution for population genetic data analysis.