A growing emphasis on systems thinking in evaluation increases the potential for conducting quality evaluation of programs nested in complex systems. Recent research efforts have led the development of strategic application of systems concepts such as the Systems Evaluation Protocol (SEP) for planning and implementation in the evaluation of nested programs. The SEP applies systems thinking concepts from evolutionary biology and developmental systems theory to program modeling, boundary analysis, and program/evaluation alignment in order to position the program and its evaluation within phases of a lifecycle that co-evolve in an ecological context. This paper presentation will discuss these theoretical concepts in depth, drawing examples from current evaluation work which utilizes a facilitated SEP.#ResearchonEvaluation #OrganizationalLearningandEvalCapacityBuilding #TeachingofEvaluation #2010Conference #SystemsinEvaluation