This paper describes a high-throughput method for quantifying gene expression in non-model organisms. The new approach — EcoP151-tagged digital gene expression (EDGE) — uses a unique tag for each expressed transcript, levels of which are determined from the number of high-throughput sequencing reads for each tag. This method avoids the need for a high-quality reference genome, as required for RNA sequencing (RNA-seq). A validation study showed that EDGE compares favourably to RNA-seq in terms of measuring transcript abundance.