Crustaceans are an ecologically and economically significant group of arthropods, being hyperdiverse and spanning marine, freshwater, and terrestrial environments. Many crustaceans are ecosystem engineers, bioindicators, and keystone species, which are integral in maintaining ecosystem health and function. The morphological, ecological, behavioural, and genetic diversity within Crustacea makes it a model group for evolutionary studies, particularly within the largest group of crustaceans, Malacostraca. In this thesis, I analyse a combination of morphological and molecular data to investigate the phylogenetics, evolutionary history, population genomics, and taxonomy of two malacostracan groups: Stomatopoda (mantis shrimps) and Decapoda (Euastacus spinifer, Giant Sydney Crayfish). First, I focus on higher-level relationships and generate the most comprehensive phylogenetic estimate of Squilloidea, the largest stomatopod superfamily, using morphological and molecular data. I show that combining these data substantially improves phylogenetic support and robustly resolves deep nodes in the tree. Then, I use whole mitochondrial genomes to generate the first molecular phylogeny of the Stomatopoda to include all seven superfamilies. I also estimate the evolutionary timescale of the group and assess the relationship between morphological and molecular rates of evolution. I then change to focus on shallow relationships and the population genomics of freshwater crayfish. Using mitochondrial sequence data and thousands of SNPs from throughout the genome of the Giant Sydney Crayfish (Euastacus spinifer), I investigate the phylogeny and population structure of the species, with implications for conservation and taxonomy. Finally, I utilise the results from population genomic analyses in association with morphology and geography to show that Euastacus clydensis, previously thought to be a synonym of E. spinifer, is a valid species, which is formally redescribed.