PopLDdecay is a tool based on VCF files that enables rapid and efficient analysis of linkage disequilibrium decay. It can calculate the LD decay distance for the entire genome or specific regions, and assess the rate and pattern of LD decay as the physical distance increases. PopLDdecay supports subgroup analysis and provides accompanying Perl scripts for visualizing the results. This tool has been published in the Bioinformatics journal and is an important tool in population genetics for studying recombination rates, selection signals, and population history.