Sexual maturation of Atlantic salmon, Salmo salar, is a complicated process that involves many variables that can act to activate and/or inhibit sexual development. Unwanted early onset of sexual maturation of Atlantic salmon is a challenge for the salmon aquaculture industry, as it has negative impacts on growth rate and product quality. Consequently, there has been a significant amount of research aiming to understand the biological mechanisms driving early salmon maturation. We present the parameters of an animal trial, coupled with RNA-seq based transcriptomics, designed to elucidate the earliest triggers which commit animals to sexual maturation. Our approach has two major components. First, animals will be photoperiod manipulated to artificially narrow the time window during which maturation is initiated. Tissue samples will be collected before, during and after the initiation event. The second component involves next generation sequencing to obtain detailed gene expression profiles. We will target the brain, pituitary and gonad tissues as the brain-pituitary-gonad (BPG) axis is central to regulating sexual maturation. We anticipate our approach has the potential to both identify the genes involved, and open new approaches to control the timing of maturation in this important production species.