Previous research on benthivorous-planktivorous ecomorph pairs of Arctic charr has shown that the repeatability into ecomorph is highly parallel and that individual traits related to head shape also show some parallelism (Adams et al., 2008; Jacobs et al., 2020). Genomic analysis to-date suggested limited genetic parallelism across lakes, with many differences in demography and colonisation history across the breadth of charr distribution (Brachmann et al., 2022; Jacobs et al., 2020; Salisbury et al., 2020). However, this previous research on parallelism between Arctic charr ecomorphs focused on the patterns of the genomic response to selection such as outlier loci, which are known to have high rates of false-positives and false-negatives and are indirect approaches to understanding morphology, strongly influenced by evolutionary genomic and demographic histories (Ravinet et al., 2017). Therefore, we lack knowledge of the genomic regions associated with key phenotypic differences in charr and the extent to which these are shared across ecomorph pairs (Elmer, 2016).