Two new species of Isospora are described from geckos from Morocco. Oocysts of Isospora altiatlantis sp. n. from the thorny-eyelidded gecko, Quedenfeldtia trachyblepharus, are subspherical to ovoidal, 28.4 (20-35) x 24.9 (19-30) mu m with a smooth, bilayered, colourless, similar to 1.2 mu m thick oocyst wall. A micropyle, oocyst residuum and polar granule are absent. Sporocysts are ellipsoidal, 11.6 (10-14) x 9.4 (8-10) mu m with smooth, similar to 0.5 mu m thick sporocyst wall. A knob-like Stieda body and relatively large, oval, homogenous substieda body are present. Sporozoites are elongate, distinctly transversally striated. Oocysts of Isospora oudrii sp. n. from the Moroccan fan-footed gecko, Pytodactylus oudrii, are spherical, 16.5 (15-18) x 16.4 (15-18) mu m with a smooth, bilayered, colourless, similar to 1 mu m thick oocyst wall. A micropyle, oocyst residuum and polar granule are absent. Sporocysts are ellipsoidal, 9.2 (9.0-10.0) x 6.3 (6-7) mu m with smooth, -0.5 mu m thick sporocyst wall. A knob like Stieda body and oval substieda body present. Sporozoites are vermiform, lying parallel within the sporocyst. Additionally, Isospora platyurusi Finkelman et Paperna, 1995 was found to be named improperly and is therefore emended to Isospora platyuri.