'unequal-gilled' is a compound of 'unequal' and 'gilled'. 'unequal' originates from Latin via Old French ('inaequalis' → 'inegal'), where the prefix 'in-' meant 'not' and 'aequalis' meant 'equal'. 'gilled' is formed from the noun 'gill' plus the past-participle/adjectival suffix '-ed'.

'unequal' passed from Latin 'inaequalis' into Old French 'inegal' and then into Middle English as 'unequal', eventually becoming the modern English 'unequal'. 'gill' (sense 'thin plate or lamella of a mushroom') developed later by analogy or extension of older senses of 'gill' (such as a narrow valley), and combined with '-ed' to form adjectival uses like 'gilled' and then compounds such as 'unequal-gilled'.

Initially, 'unequal' meant 'not equal' (from its Latin roots) and has retained that core meaning. 'gilled' originally simply denoted 'having gills'; in combination as 'unequal-gilled' it came to describe the specific condition of gills being unequal in length or arrangement.