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Nighantus are the lexicons of Ayurvedic materia medica. From the Dhanvantari Nighantu, usually dated to the eighth to tenth centuries, to the Bhavaprakasha Nighantu of the sixteenth century, they compiled plant names, synonyms and properties and became the main reference for identifying drugs. Because classical texts give few morphological descriptions, identity has been carried largely by names and synonyms, and these changed over time and between regions. This review traces how nomenclature developed in the Nighantu literature, examines how shifts in names have affected drug identity, and considers the consequences for modern research. The classical corpus contains more than 12,000 distinct Sanskrit plant names across more than 200 texts, and plant identification was learned mainly through field teaching rather than written description. Nighantus organised synonyms into groups, but their synonymy sometimes conflicts with evidence in the earlier Samhitas. Several modern confusions reflect such shifts. Brahmi is now usually equated with Bacopa monnieri, while historical analysis indicates that classical Brahmi and Mandukaparni denoted Centella asiatica. The names Bala and Pashanabheda cover several species in trade. These shifts propagate into modern research when papers, databases and pharmacopoeias map a Sanskrit name to a single species without stating the textual period or authority. We propose a critical, versioned digital lexicon that links each name to its texts, periods, commentators, regional usages and accepted botanical identities, and we recommend that research papers state the textual source and authority for every identification.