In the past decade, Cryptosporidium research has progressed considerably, often drawing on Toxoplasma gondii as a molecular model. Yet, accumulating evidence reveals that such cross-species extrapolation risks overlooking the distinctive biology of Cryptosporidium. Notably, marked metabolic differences exist not only between apicomplexans but also within the Cryptosporidium species, particularly between those infecting the stomach (C. andersoni, C. muris) and those targeting the intestines (C. parvum, C. hominis). Pathways such as polyamine and ceramide metabolism illustrate how earlier assumptions, combined with insufficient attention to species delineation, have led to an incomplete and sometimes inaccurate description of Cryptosporidium metabolism. This review examines metabolic needs and capabilities across several Cryptosporidium species to clarify evolutionary differences and highlight promising pathways for therapeutic intervention.