Forty years have passed since species of Cryptosporidium, single-cellular protozoan parasites were first recognized as significant human pathogens (as opportunistic pathogens in AIDS patients), and more than 10 years since these enteric food and waterborne parasites were recognized as major sources of debilitating infant and childhood diarrhea. In that time, our appreciation of the diversity of this species complex has grown, with a dawning appreciation of complexities in their geography and distribution among hosts. However, the discovery of myriad species and genotypes in the genus chastens researchers hoping to understand the particularities of a given infection or outbreak and underscores the limitations inherent to available diagnostic assays. Here, we briefly review foundational aspects of Cryptosporidium biology and introduce recent methodological advances that herald a newfound opportunity to characterize parasite diversity at global, regional, community, and clinical levels and call for renewed commitment to sampling these parasites, widely, in order to finally understand the processes driving parasite evolution and the practical consequences of those processes for clinical management and public health control.