For marine invertebrates that have a dispersive larval stage, the peril of the plankton is considered to be a major mortality bottleneck. Echinoderms that reproduce asexually through larval cloning have a mechanism to replenish populations through binary fission and budding with the fragmented bodies having the potential to regenerate to form a new complete larva. We followed populations of the bipinnaria larvae of the crown of thorns seastar (Acanthaster sp, COTS) through time to determine natural mortality rates and the influence of cloning as a compensatory mechanism to help maintain the number of individuals. The types of clones and mechanism of body fragmentation was also characterised. In populations generated from multiple different populations, the incidence of cloning varied, where parental source influenced cloning ability. This inherent plasticity and ability of COTS to amplify their population numbers will have important consequences with respect to the dynamics of COTS in the plankton.