The increasing amount of whole-genome sequencing (WGS) data allows us to study the evolution and transmission of Cryptosporidium spp. at the population level. Population genomics is helping us to understand the genetic structure and adaptive evolution of Cryptosporidium and the mechanism and determinants of emergence of hypertransmissible subtypes and variants. The integrated pipeline described here provides an example of the use of WGS data for evolutionary genomic analysis of Cryptosporidium.