To elucidate the role of the gonadotropins in Atlantic cod (Gadus morhua), complete coding sequences with partially or fully un-translated regions for the three subunits GPalpha, FSHbeta, and LHbeta were determined. The sequences of the corresponding genomic loci were also determined, allowing the design of mRNA-targeting quantitative PCR assays. Relative expression was analyzed during a complete seasonal sexual maturation cycle in Atlantic cod females. Increasing levels of lhbeta mRNA were observed during gonadal growth, peaking at spawning in February-March which corresponds to maximum gonadosomatic index. In contrast, both gpalpha and fshbeta gradually increased to a peak in December, two months before spawning started, and decreased in January just prior to spawning. Both mRNAs increased again and remained high during the spawning season, with a decline at the end of the spawning period, a further decrease in spent females, followed by a new gradual increase concurrent with the start of the next reproductive cycle. In addition to its role in vitellogenesis prior to spawning, FSH seems to have additional functions during the spawning period, possibly related to vitellogenesis that runs in parallel with final oocyte maturation and ovulation of the multiple batch spawner Atlantic cod.