The biogeochemcical reactions responsible for fossilized minerals preservation in ancient geological conditions are very often debatable, because little is known about the in situ processes at geo-historical period. In the present study, we describe the formation of iron ores collected in the intertidal zone of the Zhujiajian Island, Zhoushan Archipelago in the East China Sea. Morphological, mineralogical and geochemical analyses were performed on the iron ores and the surrounding geological materials. The results show that the iron ores, composed of spherical ferrihydrite and fibrous aggregates of goethite, presented morphological characteristics reminiscent of bacterial activity. The biominerization process in the seepage system is believed to represent an analogue mechanism for the biogenic formation of iron ores. The degradation of the ancient wood layer provided humic substances which accelerated the leaching process of iron from the surrounding bedrock and soils. The abundant leaching iron not only provided the sufficient iron material source, but also created the ideal conditions for the survival of the iron-oxidizing bacteria. The presence of Leptothrix-like sheaths and Gallionella-like stalks in the present-day seepage environment promoted the oxidization of Fe 2+ to Fe 3+ and the rapid precipitation of bacteriogenic iron oxides (BIOS) on bacterial sheaths and stalks, allowing the preservation of the morphological characteristics of the bacteria. As time went by, the amorphous biomineralization product (ferrihydrite) can further transfer to more crystalline goethite and therefore be preserved in the ores permanently, representing as the imprints of bacterial activity during the formation of iron ores. The present findings should help elucidate the role of bacteria in the formation of biogenic iron ores in different environments during geo-historical context.