The representation of knowledge is a process widely used in education for its potential to generate deep learning, metacognition, and also in mapping the student's cognitive structure while developing a broad spectrum of thinking skills. Notwithstanding the abovementioned benefits, the development and evolution of new digital ecologies of learning is still an unexplored field for knowledge representation systems. As part of a larger study, this article shows the process and results of a systematic review of literature on knowledge representation systems, with the purpose of identifying the foundations and main applicable instruments of digital educational environments. Among the most representative findings of this review is that despite the existence of a large number of educational experiences that have incorporated both physical and digital knowledge representation tools, their use has been restricted almost entirely to the understanding of concepts and the assessment of learning in non-collaborative environments. These findings suggest the relevance of studying the representation of knowledge in digital collaborative contexts that facilitate the development of thinking skills for the digital age, and the need for co-creation and transformation of knowledge. Together these suggest a new perspective on knowledge representation for digital ecologies of learning.