Cryptosporidium, the protozoan parasite, has several transmission routes, including anthroponotic and zoonotic transmission, as well as the foodborne way, but mainly by water. The oocysts, the resistant stage produced by Cryptosporidium, are remarkably stable, and can survive for weeks or even months in the environment. Furthermore, the infective dose is low, probably even a single oocyst can cause infection. The Cryptosporidium genus includes at least 16 species; nevertheless, only a few can cause cryptosporidiosis, an intestinal disease in human and domestic mammals. Thus, the genetic characteristics of different Cryptosporidium species became fundamental in the diagnosis, monitoring, prevention and control of infections caused by this pathogen. Unfortunately, the traditional phenotypic techniques meet with difficulties in the specific diagnosis of cryptosporidiosis, therefore the new molecular tools must be applied. The RT -qPCR method can be used to differentiate viable and dead Cryptosporidium oocysts, and the LAMP assays have advantages for detection of organisms at relatively low concentration in environmental samples; however, the NAS BA assay specifically detects as few as one oocyst of a viable human pathogenic Cryptosporidium species. Reverse line blot hybridization (RL B) has been successfully used for specific identification and for differentiation of Cryptosporidium species. Described techniques are the most promising methods for the sensitive and accurate detection, but require a considerable selection of appropriate tools, genetic markers and analytical techniques for interpretations of database. However, the applicability of most of these methods to detect Cryptosporidium species or genotypes from environmental samples needs to be evaluated and standardized.