The Bay of Prony (South of New Caledonia) represents a unique serpentinizing hydrothermal field due to its coastal situation. We used 454 pyrosequencing of 16S rRNA genes (V1-V3 region) to investigated the bacterial and archaeal communities inhabiting hydrothermal chimneys from four distant sites. These data offer an opportunity to constitute a comprehensive overview of the highly diverse microbial community in a unique hydrothermal system.