Modelling predicts that temperature and precipitation are the abiotic factors that have the biggest impact on banana production. It is clear that banana needs tropical temperatures and that it responds very early to a reduced soil water content. The stomata of banana plants also respond very sensitively to an increased Vapour Pressure Deficit even when the soil water potential is non-limiting. This sensitivity causes considerable yield losses. This chapter discusses banana physiology in relation to its agro-ecological environment and the phenotyping of traits such as sub-optimal temperature tolerance and water deficit tolerance. A workflow where the biodiversity is phenotyped in a high throughput fashion in a controlled environment and linked to molecular analysis is presented. Once interesting traits are identified, strategies are required to identify potential genetic markers that are correlated to these traits. Methods to identify the genetics behind these traits, such as genome-wide association study (GWAS), associative transcriptomics and proteomics are briefly discussed. The identification of correlations between phenotype and genetic markers will speed up future banana breeding.