Whether ooids are formed through biotic or abiotic progress seems to become increasingly controversial in recent decades. New studies indicate that the microbial effect could make important contributions to the construction, destruction and modification of ooids. Previous studies mainly focused on the organomineralization of carbonate minerals in ooids. This paper investigates the formation process of iron minerals in red oolitic grainstones of the Lower Jurassic Nieniexiongla Formation in the Tethyan Himalaya of southern Tibet. Petrographic studies and electron probe microanalysis revealed that the colorful minerals present in red ooids are hematites. Sulfur was detected in the hematites, which indicates that they were transformed from precursor pyrites. These hematites retain euhedral or framboid shapes of the pyrites. Hematite pseudomorphs distribute randomly in ooids and could not form a whole concentric layer of the ooids. Euhedral crystals usually have larger diameters than amorphous spheres and are scattered mostly in nuclei. Based on the distribution and morphology of hematites, we speculate that precursor pyrites were formed through metabolism of sulfate-reducing bacteria. Moreover, the timing of the pyrite formation was after the deposition but before the lithification. The decomposition of the microorganisms within the ooids by bacterial sulfate-reducing provides the HS-, the degradation of organic matters would produce spaces for the intrusion of pore water with sufficient Fe2+ to facilitate the pyrite deposition. In nuclei, the framboid aggregates of pyrites were transferred to euhedral crystals through continuous growth of the constituent microcrystals. Our study demonstrated organomineralization of sulfate-reducing bacteria mediated pyrites in carbonate ooids.