Poecilogony is a type of reproduction in which a species produces different types of larvae. Boccardia wellingtonensis, is a poecilogonous polychaete with females producing planktotrophic and adelphophagic larvae, in addition to nurse eggs, in the same capsule that differ in feeding behavior. It is still unclear why planktotrophs do not feed on nurse eggs during the intracapsular development and arrest its growth, while adelphophagic larvae consume nurse eggs and planktotrophic larvae inside the capsule, hatching as advance larvae or as juveniles. Here we characterized the expression of selected miRNAs from these two types of larvae and from adults in order to begin to understand the molecular mechanisms that regulate expression in this type of poecilogony. Results showed that adults and pre-hatching adelphophagic larvae have high levels of expression of miR-125, miR-87a and let-7, while adelphophages at early developmental stage had low levels of expression of miR-87b. Planktotrophic larvae showed low expression level of let-7. This work represents the first step in understanding the role of miRNAs in the development of different larval types in a poecilogonous species. We also propose to B. wellingtonensis as an interesting biological model to study the evolution of larval modes and reproductive strategies of marine invertebrates.