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Verticillium wilt, a major disease damaging cacao (Theobroma cacao) in the North East of the Democratic Republic of Congo (DRC) and in West Uganda, is caused by the soil-borne fungus Verticillium dahliae. The most effective way to manage this problem in the long-term would be by growing resistant or tolerant varieties of cacao, as done against this pathogen for other crops. This aim of the research described in this thesis was to improve understanding of the disease and how it can be managed. Genetic diversity of 33 V. dahliae isolates taken from symptomatic cacao trees in Uganda, DRC and Peru was investigated. Four distinct genetic groups were found based on different molecular markers, these groups presented morphological variations in culture and possible different virulence. The possibility of using excised parts of cacao as suitable replacements for intact seedlings or rooted cuttings in preliminary screening of the relative susceptibility of clones to V. dahliae was studied for the first time in this work. Laboratory-based assays using leaf material to assess resistance/tolerance or susceptibility to V. dahliae were developed, including quantitation of epicatechin contents, enzyme assays, fungal re-isolation and electrolyte leakage. Among those examined, the assays based on electrolyte leakage and on re-isolation of the fungus from inoculated petioles showed promise for use in classifying clones as resistant or susceptible, further sampling optimization would improve their robustness. Similar clone classification was found with these two assays: clones PA70, SCA6, GU255/V, ICS95 and Pound 7 were found resistant; ICS6, GU114/P and SPEC54/1 were found susceptible in both assays. This agreed with known field reactions of cacao clones (ICS6 and Pound 7), in vivo testing would be required for the other clones. In addition to treatments with V. dahliae conidial suspensions, treatments with pathogen elicitors and effectors contained in fungal culture filtrate were tested and would enable environmentally safer assessments of cacao resistance. In addition to using in vitro tests, breeding could be accelerated thanks to marker-assisted selection. Genomic association between genetic markers and variation in Verticillium wilt disease susceptibility was studied. One cacao marker (TcSNP1111) enabled discrimination between resistance and susceptibility. It is located at a nucleotide binding site (NBS) gene. The NBS resistance genes are known to be important in resistance of cotton to Verticillium wilt. This genomic association study needs to be extended to include more cacao clones and more markers. The protocols developed and findings of this work contribute to the understanding of the potential use of in vitro tests and association study to enhance breeding activities in cacao producing countries.