Plant breeding by research has become increasingly isolated from the plant breeding of farmers. Collaborative plant breeding (CPB) offers the possibility of bringing these two plant breeding traditions together to increase the usefulness of new crop varieties to farmers, especially small-scale farmers working in stress environments with limited external inputs. This paper presents a framework for plant breeders, social scientist, project personnel, and policy markers to understand farmer plant breeding for improving the long-term well-being of small scale farmers through CPB. Research questions are proposed based on three components of the basic biological model of plant breeding: genetic variation, environmental variation and its interaction with crop genotypes, and crop plant selection, For each component, the authors review the range of data, conclusions, and assumptions in the research literature about farmers' 1) Knowledge, 2) practice, 3) crop varieties and growing environments. The paper concludes by discussing the general implications of his approach for CPB. The framework described in this paper for understanding farmer plant breeding from a biological perspective can make a significant contribution to the success of CPB. By posing questions such as the ones suggested in this paper, a more systematic picture of farmer plan breeding, both in specific instances and in general, should emerge. Further testing of specific hypotheses based on the questions presented here is needed, especially in the context of CPB projects. This research could help farmers and plant breeders communicate more efficiently with each other, so that breeders can use their knowledge of biological theory, statistical design and analysis, and access to a wide range of genetic diversity, and farmers can use their knowledge of their crops and environments and their techniques for managing them more effectively. This collaboration should yield varieties that better meet farmers' needs and conserve crop genetic diversity in situ, thus contributing to sustainable agriculture.