The appearance of hard mineralized exoskeletons is a critical leap for animal evolution and partially lead to the explosion of diverse animals during the Cambrian, for example, molluscs. A majority of molluscs have mineralized shells to protect themselves. Despite numerous studies that have studied the remarkable mechanical properties of shells, the origin of shell formation is still elusive. Hence, this study investigated the overlooked shell proteome of chitons, which belong to polyplacophoran, Aculifera of Mollusca. By comparing the shell proteome to well-studied Conchifera groups, we inferred possible ancestral biomineralization toolkits of stem-group Mollusca. Taking advantage of the recently sequenced chiton mantle transcriptome and genome, eight core biomineralization proteins were identified by proteomics. Surprisingly, in contrast to previous thought that shell formation is convergently evolved, two important shell matrix proteins, Nacrein-like and Pif-like proteins were found to be conserved among Aculifera and Conchifera groups. Our findings identify a missed link of mineralized shell evolution in Mollusca and pose a hypothesis that stem-group molluscs have already evolved core biomineralization toolkits, which likely facilitate the formation of mineralized shells for protection that partially leads to their explosion.