Actin is a conserved cytoskeletal protein that is well studied in model organisms although much less is known about actin molecular evolution in taxonomically diverse algae. Here, we analyzed 107 novel partial algal actin sequences and report some unexpected results. First, monophyletic actin gene families in multiple, phylogenetically distantly related algal taxa contain two distinct clades of sequences. One of these clades contains highly conserved sequences, whereas the second has multiple members with a significantly elevated substitution rate. This rate difference is associated with an excess of synonymous substitutions, strongly suggesting that both isoforms are active. These results paint a novel picture of actin gene evolution in algae showing it to be a remarkably dynamic system with duplication, homogenization, and potential functional diversification occurring independently in distantly related lineages.