Understanding the true nature of extra-terrestrial water and organic matter that was present at the birth of our solar system, and their subsequent evolution, necessitates the study of pristine astromaterials. In this study, we have studied both the water and organic contents from a dust particle recovered from the surface of near-Earth asteroid 25143 Itokawa by the Hayabusa mission, which represents one of the most uncontaminated astromaterial samples in Earth’s collection. The organic matter is presented as both nanocrystalline graphite and disordered polyaromatic carbon with high D/H and 15N/14N ratios (δD = +4,868 ± 2,288‰; δ15N = +344 ± 20‰) signifying an explicit extra-terrestrial origin. The contrasting organic feature (graphitic and disordered) substantiates the rubble-pile asteroid model of Itokawa, and offers support for material mixing in the asteroid belt that occurred in scales from small dust infall to cartographic impacts of large asteroidal parent bodies. Our analysis of Itokawa water indicates that the asteroid has incorporated D-poor water ice at the abundance on par with inner solar system bodies. The asteroid was metamorphosed and dehydrated on the formerly large asteroid, and was subsequently evolved via late-stage hydration, modified by D-enriched extraneous organics and water derived from a carbonaceous parent body.