Crustose coralline algae (CCA) are calcifying red macroalgae that reef build in their own right and perform essential ecosystem functions on coral reefs worldwide. Despite their importance, limited genetic information exists for this algal group. De novo transcriptomes were compiled for four species of common tropical CCA using RNA-seq. Sequencing generated between 66 and 87 million raw reads. Transcriptomes were assembled, redundant contigs removed, and remaining contigs were annotated using Trinotate. Protein orthology analysis was conducted between CCA species and two noncalcifying red algae species from NCBI that have published genomes and transcriptomes, and 978 orthologous protein groups were found to be uniquely shared amongst CCA. Functional enrichment analysis of these ‘CCA-specific’ proteins showed a higher than expected number of sequences from categories relating to regulation of biological and cellular processes, such as actin related proteins, heat shock proteins, and adhesion proteins. Some proteins found within these enriched categories, i.e. actin and GH18, have been implicated in calcification in other taxa, and are thus candidates for involvement in CCA calcification. This study provides the first comprehensive investigation of gene content in these species, offering insights not only into the evolution of coralline algae but also of the Rhodophyta more broadly.