The morphology and infectivity of the oocysts of a new species of Cryptosporidium from the faeces of the red kangaroo (Macropus rufus) are described. Oocysts are structurally indistinguishable from those of Cryptosporidium parvum. Oocysts of the new species are passed fully sporulated, lack sporocysts, and measure 4.5-5.1 μm (mean=4.9) × 3.8-5.0 μm (mean=4.3 μm) with a length to width ratio 1.02:1.18 (mean 1.14) (n=50). Oocysts were not infectious for neonate ARC Swiss mice. Multi-locus analysis of numerous unlinked loci demonstrated this species to be distinct (90.64%-97.88% similarity) from C. parvum. Based on biological and molecular data, this Cryptosporidium infecting marsupials is proposed to be a new species Cryptosporidium fayeri n. sp.