In this study, two diverse scientific areas of research, namely, biological-chemical and public administration, were drawn upon to find an answer for improved risk governance of genetically modified organisms (GMO/GM) and pesticides. The need for such a study appeared from the constraints experienced with regulatory approval of GMO crops in South Africa. The knowledge gained from research on risk governance of GMOs could also be applied to pesticides. Protracted procedures causing delays in approval and increasingly stringent regulatory requirements of GMOs resulted in negative implications for research, development and commercialisation. Approval of several South African co-developed GMOs has been delayed or rejected that resulted in withdrawal or reducing of research activities, apart from appeals against decisions. The objective of the study was to identify some of the reasons for delays as experienced in risk assessments and to propose remedial actions, including the critical interface between role players in risk governance. The approach taken in this research was to obtain, by means of a questionnaire, a broad view of risk governances of GMOs as measured with criteria of good governance experienced by scientists of biotechnology and related disciplines. This was followed by another questionnaire with focus on one specific area that caused delays for GMO permit applicants. The investigation included analysis of South African legislation, guidelines and interviews. The research on risk assessment narrowed down to the two areas, illustrated by South African applicable case studies, namely, food risk/safety assessment of GMO cassava and environmental risk assessment of GMO sorghum. Approaches to improve assessments are being recommended. Uncertainty in risk assessment is an important reality because of humankind‘s limited knowledge of nature. Uncertainty is further addressed by precautious management, described as the precautionary principle is a norm legislated by the South African government in line with international agreements (the Cartagena Protocol on Biosafety). The terminology, precautionary approach and principle are used interchangeably in literature. The application of the precautionary principle in South African legislation and the difficulty that could be experienced in decision making are illustrated in the case study on ‗possible unintended changes in endogenous allergens‘ in GMO maize. The research showed the importance of timely risk communication between risk assessors, risk managers (decision makers) and stakeholders in advance of the commencement of risk assessment. The importance of timely consideration of socio-economic impact of GMOs and pesticides is touched on. Risk governance structures, for both GMOs and pesticides are proposed, based on the most democratic and transparent governance models taking into consideration the European initiatives for improved risk governance. This included an interface for interaction among role players, namely, risk assessors, risk managers, scientists and stakeholders. The up-front role of an array of scientists, as the most trustworthy communicators in contentious scientific issues, is of specific importance because of the fast developing and very broad field of genetic modification of many crops. South Africa‘s national research institutes should play a much bigger role as scientific advisors in scientific risk policy making and framing for risk assessments. It is of great importance that risk assessments are focused on risks and not on the gathering of bucketsful of data; therefore, training in approaches to assessment of risk should be a priority. To achieve improvement on risk governance, the importance of policy development and the roles of all participants should be clear. Proposals for future research cover the many aspects that comprise trust in governance and the increased awareness of consumers and stakeholders of environmental risks and food safety. This study also paves a way for research on governance of phytopesticides and phytomedicines because of growing interest in these rich sources of new information that could be of great benefit to mankind.