Biodiversity is said to be the “heart of sustainable agricultural systems”. Biodiversity research is envisioned to provide a better understanding of development issues so that better policy responses, management practices and actions will ultimately redound to a better quality of life for all, especially the poor. It is in this light that the Philippines-Netherlands Biodiversity Research Programme for Development is revisited and analyzed in this paper. This and other similar projects provide lessons for capacity development at the community, national, regional and international levels. To proceed with its analysis, the paper fleshes out the framework of sustainable development, situating the role of biodiversity in determining the pathway of development. As shown, biodiversity, as an element of the natural resource base, and in concert with technology and sociocultural factors, will continue to be relevant in a rapidly changing and increasingly globalized world. It also presents the sustainable livelihood framework to illustrate that biodiversity alone, being only one component of natural capital, cannot alleviate poverty if nothing is done with the other capital assets. One important lesson gleaned from the analysis of biodiversity research is that not all biodiversity is good. The key is to better understand the interactions between various levels and how these can be harnessed into positive interactions to produce a productive, stable and sustainable resource base. Another emerging lesson is that biodiversity can be conserved in agroecosystems if the poor resource users can be enabled to use it to improve their assets in the context of the sustainable livelihood framework. The effective management and conservation of agricultural biodiversity can be achieved through product value addition and link to market, germplasm enhancement, and participatory plant breeding, among others.