This manuscript reflects on the affordances and limitations of methodological approaches commonly adopted by science education researchers examining learner identities. Our aims are to unpack the relative strengths and weaknesses of such approaches and note their respective prevalence. In so doing, we identify and critique studies which we consider exemplify the different approaches and, in turn, note the direction of fruitful developments and the nature of key challenges. From our review of the field, we suggest that three discrete methodological approaches can be identified: macro-studies within a psychological tradition; macro-studies within a sociological tradition; and micro-studies within an interpretive tradition. Our review comprised a critical analysis of papers included in the Web of Science databases published between 1998 and 2018. A total of 198 papers examining aspects of learner identity relating to science were identified. Of these, the majority (146) were categorised as micro-studies within an interpretive tradition. We discuss the implications of methodological choices for the advancement of understanding and further note ambiguities in the field particularly in relation to the ways in which learner identity research is conceived. We also raise questions for the field relating to the ways in which findings may be scaled, and how the field might develop to allow stronger theoretical and conceptual coherence.