The most recent advances concerning the phylogeny and evolution of calcareous sponges (Calcarea or Calcispongia) are reviewed here, in the light of the history of taxonomy of the group and conceptions about its evolution, starting from Haeckel’s works at the end of the 19th century. Calcisponge phylogeny has recently started to be addressed using modern tools of phylogenetic reconstruction: cladistic analysis of morphological characters and molecular phylogeny (so far using 18S and 28S rDNA sequences). The monophyly of calcareous sponges is strongly supported in these works, as is their subdivision into two clades, Calcinea (whose proposed synapomorphy is the basal position of nuclei in choanocytes, with no relation to the flagella) and Calcaronea (whose possible synapomorphy is the formation of the amphiblastula larva through the original process of eversion of the stomoblastula). While the molecular phylogeny of Calcinea is still in its infancy because of insufficient taxonomic sampling, several lines are emerging for the phylogeny of Calcaronea, and these are in strong disagreement with the classification issued from the “traditional” morphological approach. Phylogenetic hypotheses also permit the reconstruction of morphological character evolution, which appears complex and subject to a high level of homoplasy.