Metamorphosis involves a complex network of genes that orchestrate a perfectly timed reorganization of one body form to another. The molecular pathways that start to unravel for an increasing number of species show that there exists great diversity among different species, as would be expected by their wide range of life histories and transformation strategies. The metamorphosis process could account for a considerably high percentile of transcribed sequences over a short period of time, with the genome encoding for different life forms. Such important changes in expression patterns for a high number of genes pose a challenge for accurately assign each gene to a function. Several key conserved factors are consistently expressed and can be placed at the center of metamorphosis, including the mechanisms involving the molt hormone, 20 Hydroxy-Ecdysone, and the juvenile hormone. Yet, many additional factors are not characterized, remain unannotated, or do not have a function assigned. This manuscript provides several examples of how an integrated omics approach can develop further insights into crustacean metamorphosis and eventually lead to discovery of key factors for metamorphosis.