Aphanic species are those within a taxonomic complex that may not be readily distinguishable from other sympatric species. The existence of these species is becoming apparent at an increasing rate through the use of technological tools like molecular genetic analyses. A lack of clarity on the definitions of terms used to describe similar species, how these species are identified, and how prevalent they are can confound identification, description, and management of these organisms. This review collects and defines the terms used to describe these hidden species and suggests the use of the term aphanic for situations where additional information (and therefore classification) is not yet known. The review also addresses species identification methods and upholds the recommendation that newly proposed aphanic species should be validated by the use of two or more methods, such as morphological assessments alongside DNA identifications. Additionally, five historical case-study examples lead to the recommendation that management of newly-discovered aphanic species should remain managed under the species it is found within until information relating to each species’ risk is understood. Information must then be pushed to and evaluated by the appropriate stakeholders to ensure effective management strategies.