The mechanisms of contraction of molluscan striated and smooth muscles differ from those in vertebrates. Molluscan striated muscles adopt a myosin-linked regulation, unlike vertebrates. Smooth muscles in these species show a unique form of contraction, in which the tension is maintained for a long time with little energy consumption, called catch. The available gene information is insufficient to elucidate the mechanism of contraction of molluscan muscles at the molecular level. BLAST searching was thus used to annotate genes encoding proteins related to muscle contraction in the completely determined genome of the pearl oyster Pinctada fucata using partial nucleotide sequences obtained by 3′ RACE. We identified genes that encode components of the thick-filament, such as myosin heavy chain, myosin essential and regulatory light chains, paramyosin and twitchin; of the thin-filament, such as actin, tropomyosin, troponin-T, troponin-I, troponin-C and calponin; and the PKA catalytic subunit, which is a key player in the regulation of catch contraction. The analysis indicated that isoforms of myosin heavy chain, paramyosin, and calponin are produced by alternative splicing.