Here, we examine transcriptome-wide divergence and polymorphism in the marine copepod Tigriopus californicus, a species where allopatric evolution has led to replicate sets of populations with varying degrees of divergence and hybrid incompatibility. These data is accompanying the paper entitled "Transcriptome-Wide Patterns of Divergence During Allopatric Evolution", by RJ Pereira, FS Barreto, NT Pierce, M Carneiro and RS Burton, published in Molecular Ecology.