Fusarium wilt disease caused by pathogenic F. oxysporum isolates are major constraints to global legume production, accounting for losses up to 90% annually, and are significant biosecurity threats to Australia’s major legume industries, particularly chickpea worth ~$1B (2016). Substantial crop losses, no curative treatments and persistence of pathogen spores in soil ranks F. oxysporum high on the list of globally important plant pathogens. Strict quarantine regulations prevent import of legume-infecting isolates into Australia for research purposes. To reduce the probable impact of this pathogen on Australian legume industries we developed a model pathosystem using the model legume Medicago truncatula and a F. oxysporum f. sp. medicaginis isolate (Fom) with the aim of providing resources and expertise to combat disease incursion. To dissect pathogenicity mechanisms we generated a high quality Fom genome assembly including almost near complete assembly of its predicted pathogenicity chromosome. This latter scaffold sequence contains all Fom homologs of the tomato F. oxysporum f. sp. lycopersici Secreted In Xylem (SIX) pathogenicity-associated genes. Using genomic location and relative increase in in planta expression as an indicator of key roles in pathogen attack, high-depth RNA-sequencing of the Fom transcriptome at various stages of host infection and in vitro confirmed expression of candidate SIX effectors and facilitated prediction of novel candidate effectors. Further novel machine-learning based effector prediction algorithms developed in CSIRO were applied to determine a Fom pathogenicity effector set which assessed against the genomes of other Fusaria and those pathogenic on legumes (e.g. F. oxysporum f. sp. ciceris; chickpea infecting), identified 5 candidate effectors highly conserved amongst legume-infecting isolates. These effectors may be useful tools for pre-emptive breeding of Australian chickpea cultivars to protect against bioinvasion of globally destructive F. oxysporum f. sp. ciceris isolates.