Usable genomic data is essential to underpin research in blossoming model organisms. Parhyale hawaiensis, with an estimated genome size of 3.6 Gb, represents one such system amongst the understudied Malacostraca Class of the Crusatcea. Parhyale has already been established as a tractable model system for studies of developmental mechanisms and more recently adult regeneration. As well as harbouring some of the most exciting examples of body plan adaptations the Malacostraca include the crustacean food crop species that are important sources of income for several low and middle-income countries. Recently there has been an increase in pathogen and immunity related aquaculture problems in these species as farming has intensified. Here we assemble, annotate and analyse the genome of this species and highlight key features relevant to broad collection biomedical research areas, including immunity and lignocellulose digestion for biofuel research. The Parhyale genome is highly repetitive and polymorphic, including many polynucleotide insertions and deletions that lead to separate assembly of alleles. The genome sequence allows annotation of all key signalling pathways, small non-coding RNAs and transcription factors that will underpin ongoing functional studies. We also analyse the immunity related genes of Parhyale as an important comparative system for the major Malacostracan food crops. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion, suggesting this ability may predate the diversification of this lineage. Bisulfite sequencing established genome wide DNA methylation patterns in Parhyale, which appear to encompass both gene bodies and upstream regions in contrast to the pattern observed in insects. Finally, we provide an example of how the genome sequence provides an important resource for functional studies by making use of CRISPR-Cas9 genome editing approaches to study gene function. Our data provide an essential resource for further development of the Parhyale model system for developmental studies. The first Malacostracan genome sequence will underpin ongoing comparative work in important food crop species and biofuel research pursuing efficient lignocellulose digestion mechanisms.