Myostatin (MSTN), a member of the transforming growth factor (TGF)-beta family, is a potent negative regulator of skeletal muscle growth and maintenance. The MSTN prodomain inhibits MSTN biological activity. The rotifer Brachionus rotundiformis is an excellent primary live feed for fish larvae in aquaculture; however, it is not known whether the rotifer expresses MSTN and the MSTN prodomain along with its activity. The objective of this study was to examine the effects of recombinant MSTN prodomains. Individual cultures of the rotifer B. rotundiformis were carried out to determine the effect of recombinant MSTN prodomains (pMALc2x-poMSTNpro and pMALc2x-sMSTNpro) on the pre-reproductive phase, reproductive phase, post-reproductive phase, offspring, lifespan, fecundity, and male ratio. In addition, a population culture of the rotifer was performed to confirm the effects of pMALc2x-poMSTNpro and pMALc2x-sMSTNpro on population growth. The results showed that the rotifer treated with pMALc2x-pMSTNpro had a reduced pre-reproductive phase at higher concentrations (1, 2, and 4 μg/ml) compared to the non-treated control group. Moreover, the pMALc2x-sMSTNpro treated rotifer effectively decreased the pre-reproductive phase at a lower concentration (0.25 μg/ml) compared to the pMALc2x-pMSTNpro treated and control group. Interestingly, pMALc2x-poMSTNpro and pMALc2x-sMSTNpro significantly increased the population of B. rotundiformis.