Subsistence Bhutanese farmers spread across different agro-ecological zones maintain large species and varietal diversity of different crops in their farm. However, no studies have been undertaken yet to assess why farmers conserve and maintain large agro-biodiversity, the extent of agro-ecological richness, species richness, estimated loss of traditional varieties and threats to the loss of on-farm agro-biodiversity. Information on the number of varieties cultivated by the farmers for six important staple crops were collected from nine districts and twenty sub-districts spread across six different agro-ecological zones of the country to understand farmers reasons for maintaining on-farm crop diversity, estimate agro-ecological richness, species richness and the overall loss of traditional varieties, to know the famers’ level of awareness on climate change and the different threats to crop diversity. The results from this study indicated that an overwhelming 93% of the respondents manage and use agro-biodiversity for household food security and livelihood. The average agro-ecological richness ranged from 1.17 to 2.26 while the average species richness ranged from 0.50 to 2.66.