Three new species of Isospora Schneider, 1881 are described from agamid lizards, Isospora cannoni n. sp. in Diporiphora australis from northern Queensland, Australia, I. choochotei n. sp. in Calotes mystaceus from northern Thailand, and I. deserti n. sp. in Agama pallida from Israel. I. cannoni oocysts are subspherical, 20–25 × 22.5–27.5 μm with two ovoid sporocysts, 14–15.5 × 10–11.5 μm. I. choochotei oocysts are spherical to subspherical, 24–32 × 28–32.5 μm with two ovoid sporocysts, 11 × 15.5–18 μm. I. deserti oocysts are spherical, 25–28 μm in diameter with two ovoid sporocysts, 10–11 × 14–17.5 μm. All species had sporocysts with Stieda bodies and underwent endogenous development in the nucleus of the host gut epithelial cells. At completion of merogony and gamogony, the host nucleus was reduced to a thin envelope. The significance of endogenous stage characteristics in Isospora taxonomy is discussed.