Cassava is one of the most important starchy root crops in the tropics due to its adaptation to marginal environments. This study examines the genetic architecture of 14 continuous and categorical traits, including defense against biotic stresses, agro-morphological and quality-related traits. The paper provides a catalogue of genomic loci associated with the 14 traits, a list of favourable alleles for each trait-locus combination and candidate genes located within the identified loci. Understanding the genetic architecture of variation in the studied traits is an important step towards the development of molecular tools to accelerate the transfer of favourable alleles into farmer-preferred varieties.