The lack of unequivocal sponge fossils before the Cambrian despite their probable deep origin during the Cryogenian period has been a conundrum to geologists. Their impact on the dramatic evolution of ecosystems and the seawater silica cycle during the Ediacaran-Cambrian (E-C) transition is also speculative. In this study, abundant sponge spicules and spicule-like structures that probably represent original sponge fossils were recovered from four sections of the E-C boundary interval in the Yangtze Gorges, South China. The paleontological and geochemical data presented herein provides evidence for a continuous distribution of relatively abundant sponge spicules, some even forming spiculites, as well as the earliest biogenic deposition of silica by metazoans in the Ediacaran-Cambrian boundary interval. These results further confirm that a biological takeover of oceanic dissolved Si co-occurred with the evolution of silica biomineralization in the E-C interval, resulting in the widespread deposition of biogenic chert. Hydrothermal input in spicule-bearing cherts is also observed. Such hydrothermal activity might have favored the blooming of sponges through significant nutrient supply. These results provide the first conjunction of geochemical and paleontological proxies in support of previous models considering that sponges, by ventilation, filtration and oxygenation of seawater, were important ecosystem engineers of the E-C bioradiation event and of the related establishment of modern-type ecosystems.