The main reason for this difficulty is that standard genetic manipulations -whether through stable mutagenesis or through factors injected in the egg- generally lead to embryonic phenotypes or lethality, and their larvae would thus be abnormal or not survive to the metamorphic stages under study. More general treatments of larvae likewise cause larval phenotypes independent of their impacts on the structures in larvae fated to form the juvenile: namely, the imaginal discs in holometabolous insects. Also, years of detailed studies in insects led to the ability to culture these imaginal disks in vitro, thus illuminating the previously obscure events of specification and differentiation of presumptive adult structures. We are not aware of any such techniques having been devised for a marine invertebrate, though new functional genomics approaches –that allow the specific manipulation of genes and gene products– should allow more incisive investigations into marine invertebrate larval development, including settlement and metamorphosis. Here we report on our success in targeted manipulation of juvenile development in purple sea urchin larvae. Using a new class of morpholino oligonucleotides that readily cross cell membranes, we describe a technique where we can reliably inject these compounds inside juvenile rudiment tissues of temporarily immobilized late stage S. purpuratus larvae. As a proof of concept, we injected vMOs designed to knock down the expression of p16 and p58b, two genes involved in skeletal elongation in sea urchin embryos. We report a significant decrease in the elongation rate of adult spines in both p16 and p58b-injected larvae when compared to those injected with the control vMO, a carrier control and an uninjected control. Along with our morpholino injections, we also injected rhodaminated dextran as a tracer. These Screening Libraries injections resulted in accumulation of rhodamine into different compartments of the developing rudiment, allowing for visualizations of developing juvenile tissues at a level of detail not previously described. Complex life cycles have evolved repeatedly in animals and non-animals alike. In the majority of coastal marine invertebrates, the most dramatic life cycle transition involves a metamorphosis from a planktonic larva to a benthic adult. This metamorphic transition has profound implications for the ecological stability of marine communities, gene flow among them, and their recovery following disturbance. Furthermore, invertebrate metamorphoses are fascinating developmental events in their own right, where the adults often differ morphologically, behaviorally and ecologically from their corresponding larval forms. Echinoderms such as the purple sea urchin, Strongylocentrotus purpuratus, represent notable examples. Despite the relevance and interest in such transformations across invertebrates and within echinoderms, we have limited mechanistic understanding of the developmental and physiological processes that regulate marine invertebrate metamorphoses. One major impediment to gaining such understanding is the difficulty inherent in manipulating genes in late stage larvae without causing embryonic phenotypes at earlier stages.