Somatic embryogenesis, an efficient regeneration system that is being used successfully in genetic transformation, can be coupled with mutation induction to breed for cassava varieties with desired traits. The embryogenesis system requires the initiation of totipotent cells which can be used as targets for mutagenic treatments. However, initiation of these totipotent cells is low, highly genotypic dependent and has low plant conversion rate. Thus, for its successful application in mutation induction, the system needs to be optimised to overcome these drawbacks. To optimise the system, totipotent cells are initiated on embryo initiation medium (EIM) which consisted of Murashige and Skoog (Physiol Plant 15:473-497, 1962) basal salts supplemented with picloram and 2,4-dichlorophenoxy acetic acid (2,4-D) to produce callus. After 21 days, calli produced are cultured for embryo maturation on maturation medium (EMM) or can also be treated with mutagenic agents for mutant induction. The resulting primary embryos are recycled three consecutive times, each by fragmentation of the cotyledons followed by culture on embryo initiation medium to produce more matured embryos. Somatic embryos produced are then successfully converted into plants by abscisic acid pretreatment in embryo maturation medium or by air desiccation under the laminar flow hood. The methodology described offers optimised, reproducible procedures of somatic embryogenesis for its incorporation into mutation breeding programmes in cassava.