In this study, we investigated the genomic underpinnings of head and body shape morphology in replicate ecomorph pairs of Arctic charr across four independent lakes in Scotland. First, we determined the extent of phenotypic parallelism in head and body shape morphology across ecomorph pairs. We examined these two traits separately as they are known to involve different axes of ecological specialisation and can have different genetic bases (Boulding et al., 2008; Küttner et al., 2014; Smith et al., 2020). Second, we investigated the genome-wide underpinnings of these phenotypes by identifying SNPs strongly associated with head shape variation and body shape variation. We then evaluated the genomic organisation of these head shape- and body shape-associated SNPs, specifically to determine if they were distributed widely across the genome, co-localised in genes or genomic regions, or within known salmonid QTLs. To do this, we updated and augmented an existing QTL database (Jacobs et al., 2017) and mapped this to the orthologous location in the Salvelinus sp. genome. Third, we examined evolutionary genomic background by analysis of selection on those loci we found to be associated with head shape and with body shape. Shared signals of selection and elevated differentiation and divergence in independent ecomorph pairs would suggest similar processes across evolutionary replicates. Finally, we synthesised the findings to identify shared genomic underpinnings and similarities in phenotypic divergence between head and body shape, as two interlinked components of ecomorph.