Evolution of both free-living and sessile chordates is closely associated with the acquisition of tadpole-like body plan. Our ancestor adopted a new style of swimming by beating of tail formed by notochord and muscle. Comparison of genomes is expected to provide insight into the molecular genetic basis of such novel features of chordates. To infer the evolutionary process in muscle structural proteins, we estimated gene trees based on sequences derived from genome data representing major deuterostome lineages. In order to reconstruct the gene trees employing exhaustive sequence sampling, we constructed an analysis pipeline consisting of two-step approach: 1) selection of ortholog candidates using BLAST search and neighbor joining analysis, and 2) estimation of gene trees using maximum likelihood analysis. The resultant gene trees suggest that muscle protein isoform families of chordates (e.g, actin and myosin heavy chain) tend to be the products of independent gene duplications in each lineage. In most cases, the genes in ascidians, apart from those in lancelets and other deuterostomes, form a sister group with a clade including highly diversified genes in vertebrates. Our results suggest that the tadpole-like body plan, originated before the separation of ascidian and vertebrate lineages, diverged independently by increasing the number of genes within each lineage.