Capsicum chinense is recalcitrant in in vitro morphogenesis. No efficient, reproducible somatic embryogenesis regeneration system exists for this species, impeding regeneration from transformed cells. An indirect somatic embryogenesis protocol is developed using mature C. chinense zygotic embryo segments (ZES). The ZES cultured in semi-solid Murashige-Skoog (MS) medium supplemented with 8.9 µM naphthaleneacetic acid, 11.4 µM indoleacetic acid and 8.9 µM 6-benzylaminopurine, developed an embryogenic callus and 8% of the calli developed somatic embryos. Torpedo-stage somatic embryos were detached from the callus and subcultured in semi-solid MS medium without growth regulators, producing a 75% conversion rate to plantlets with well-formed root tissue. Histological analysis showed the developed structures to have no vascular connection with the callus and to be bipolar, confirming that this protocol induced formation of viable somatic embryos from mature C. chinense ZES. All acclimated plantlets survived under greenhouse conditions. This protocol will facilitate regeneration of genetically transformed plants using either biolistics or Agrobacterium tumefaciens approach.