One important aspect of sustainability in biomass production concerns biodiversity, which is central in ecology and natural resource management. Biodiversity has both intrinsic value and instrumental value to humans and is important for ecosystem stability and provision of the numerous ecosystem services that are essential for human survival. Studies indicate that human activities have increased the species extinction rate, primarily through (i) habitat destruction, degradation and fragmentation; (ii) invasive species; (iii) pollution, including human induced changes in climate; and (iv) over-exploitation of essential resources, including overhunting. Bioenergy expansion may influence most of the causes of increased species extinction rate. The aim of this study is to assess the biodiversity considerations in certification standards for sustainable biomass production. In total, 23 standards for forest management, agricultural management and production of bioenergy crops, were included in the assessment. A harmonization of different definitions of biodiversity was made based on considering principles of conservation biology, in order to identify aspects of biomass production of relevance for biodiversity. Based on the identified aspects, a reference standard was constructed and all included standards were compared with this reference standard as a way to establish how the different standards showed similarities and differences regarding how biodiversity was considered. Restrictions on specific ecosystems conversion were also assessed for all standards. The results showed a noticeable variation in how the certification standards consider aspects of relevance for biodiversity. There was both a variation among similar standards and between different types of standards. In general, the bioenergy crop standards had the strictest rules and restrictions in relation to biodiversity followed by the forest management standards. The agricultural management standards had more lax rules and restrictions. It is proposed that biodiversity conservation in production of sustainable biomass can be improved by further developments of the certification standards.