The paper presents the first-hand results of a biodiversity assessment process carried out within the BioBio project. Focus group methodology was used to explore how farmers relate to biodiversity and what kind of benefits they realize. In each of the three case study areas one focus group was dedicated to organic farmers and another one to conventional farmers in order to compare their perceptions. Our results suggest that biodiversity is not an independent, purely scientific concept for farmers, but it is considered through their everyday life and farming practices. When farmers think about biodiversity they address species and habitat diversity the most frequently. Complexity is also an important component of biodiversity for them, and the complex nature of biodiversity is often linked to their personal philosophical and spiritual commitments. Farmers – regardless of being organic or conventional ones – attribute a mixture of values to biodiversity. Beside economic benefits, the ethical and social values attached to biodiversity are also crucial and are often more directly acknowledged. These results warn us that scientific concepts become inherently value-laden when we put them into the local context. Hence, scientists should be aware of the various contexts of valuation and should understand how participants conceptualize the subject of valuation before choosing the appropriate method of valuation. Furthermore, the large variety of different values farmers attached to biodiversity reinforces that monetary valuation methods may have limits in biodiversity valuation because they may restraint the range of benefits acknowledged by farmers.