Sponges (phylum Porifera) were prolific reef-building organisms during the Paleozoic and Mesozoic approximately 542 to 65 million years ago. These ancient animals inherited components of the first multicellular skeletogenic toolkit from the last common ancestor of the Metazoa. Using a paleogenomics approach, including gene- and protein-expression techniques and phylogenetic reconstruction, we show that a molecular component of this toolkit was the precursor to the alpha-carbonic anhydrases (alpha-CAs), a gene family used by extant animals in a variety of fundamental physiological processes. We used the coralline demosponge Astrosclera willeyana, a "living fossil" that has survived from the Mesozoic, to provide insight into the evolution of the ability to biocalcify, and show that the alpha-CA family expanded from a single ancestral gene through several independent gene-duplication events in sponges and eumetazoans.