Scholarly discourse on sacred natural sites (SNS) has focused on ecological significance, associated impacts and traditional practices as the instruments of resource governance and management. As a result, little scholarship has examined the role of spirits in governing and managing SNS; these are inhabited by deities or numina, commonly known as nature spirits. This study aims to provide evidence of the importance of governance by spirits as a prerequisite for protecting biophysical resources. Data were collected through semi-structured interviews and observation. The respondents were selected through a purposive sampling approach. The author also attended a funeral that was held at one of the SNS discussed in this article. The collected data were analysed through a thematic content analysis. The study shows that, for biodiversity to be protected, there should be a good relationship between humankind and the spirits. The spirits place behavioural demands on humankind involving the performance of rituals. Ritual behaviour empowers the spirits to be placed as owner of SNS and to guard against intruders. In return, humankind receives blessings, protection, patronage and governance. The governance by spirits is complemented by traditional practices. I conclude that governance by spirits should be recognised both locally and internationally.