The research described in this thesis is focused on biominerals of calcium carbonate, in particular the organic matrix embedded in the mineral phase of mollusk shells and corals skeletons, which directly controls the biocalcification process in these organisms. In this scope, the organic matrix proteins are considered as key components of the biological control over mineralization. Since the first report by Miyamoto and co-workers of a protein (Nacrein) from the mollusk shell of the pearl oyster in 1996, many proteins in shells and other mineralized structures were identified by a one-per-one approach using classical molecular biology and biochemistry techniques. Until recently, the existing information was manageable and consisting of some proteins with very specific signatures: secretion signals, acidic domains, carbonic anhydrases, low complexity regions, and not much else. With the entrance in the post-‘omic’ era, the fields of genomics, proteomics and transcriptomics also reached the biomineralization field and have allowed the scientific community to discover a much wider range of proteins taking part in the control of biocalcification mechanisms. These large newly identified protein datasets, are often difficult to interpret in light of the current models of calcification. The main goal of this dissertation is to give a contribution in this context. Apart from identifying several new proteins by means of high-throughput technologies, we present a careful analysis of the results and further interpretation from functional and evolutionary perspectives.