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The purpose of this article is to describe how to use Phenomenography and the Variation Theory of Learning to conduct online education research which will help answer the “why” of a phenomenon and not simply the “what”. The backdrop of this paper is an ongoing study investigating the experience of teaching online secondary science. This study will be used to help elucidate the steps required to conduct effective phenomenographic interviews and how best to employ the Variation Theory of Learning to identify structures of awareness. Issues of reliability and validity particular to this methodology are also discussed.