The predominance of sexual reproduction indicates that it must confer profound benefits, considering its significant costs relative to asexuality. However, definitively determining whether a lineage engages in sex is often complicated by the potential for cryptic sex, especially among unfamiliar organisms. Here we consider the strengths and weaknesses of various molecular- and organismal-based approaches for recognizing signs of sex and describe their applications and relevance to evolutionary biology. We review recent studies that use these methods; some analyses even dispute several 'ancient' asexual taxa, and suggest they are recently derived or might be covertly sexual. More broadly, a better understanding of which organisms have sex and how they do it will deepen our understanding of the distribution, maintenance and evolution of sexual reproduction.