The morphological, biological, and molecular characteristics of Cryptosporidium piscine genotype 1 from the guppy (Poecilia reticulata) are described, and the species name Cryptosporidium huwi n. sp. is proposed to reflect its genetic and biological differences from gastric and intestinal Cryptosporidium species. Oocysts of C. huwi n. sp. over-lap in size with Cryptosporidium molnari, measuring approximately 4.4–4.9 µm (mean 4.6) by 4.0–4.8 µm (mean 4.4 µm) with a length to width ratio of 1.04 (0.92–1.35) (n = 50). Similar to C. molnari, C. huwi n. sp. was identified in the stomach only and clusters of oogonial and sporogonial stages were identified deep within the epithelium. However, phylogenetic analysis of 18S rRNA sequences indicated that C. huwi n. sp. exhibited 8.5–9.2% and 3.5% genetic distance from C. molnari isolates and piscine genotype 7 respectively. At the actin locus, the genetic distance between C. huwi n. sp. and C. molnari was 16.6%. The genetic distance between C. huwi n. sp. and other Cryptosporidium species at the 18S locus was 13.2%–17% and at the actin locus was 18.9%–26.3%. Therefore C. huwi n. sp. is genetically distinct from previously described Cryptosporidium species.