Despite the increasing trend worldwide of integrating indigenous and scientific knowledge in natural resource management, there has been little stock-taking of literature on lessons learned from bringing indigenous knowledge and science together and the implications for maintaining and building social-ecological system resilience. In this paper we investigate: (1) themes, questions, or problems encountered for integration of indigenous knowledge and science; (2) the relationship between knowledge integration and social-ecological system resilience; and (3) critical features of knowledge integration practice needed to foster productive and mutually beneficial relationships between indigenous knowledge and science. We examine these questions through content analyses of three special journal issues and an edited book published in the past decade on indigenous, local, and traditional knowledge and its interface with science. We identified broad themes in the literature related to: (1) similarities and differences between knowledge systems; (2) methods and processes of integration; (3) social contexts of integration; and (4) evaluation of knowledge. A minority of papers discuss a relationship between knowledge integration and social-ecological system resilience, but there remains a lack of clarity and empirical evidence for such a relationship that can help distinguish how indigenous knowledge and knowledge integration contribute most to resilience. Four critical features of knowledge integration are likely to enable a more productive and mutually beneficial relationship between indigenous and scientific knowledge: new frames for integration, greater cognizance of the social contexts of integration, expanded modes of knowledge evaluation, and involvement of inter-cultural "knowledge bridgers."