'fluorophore' originates from New Latin and Greek, specifically the New Latin/Latinate element 'fluor-' (from Latin 'fluorescēre') where 'fluor-' meant 'to emit light (by fluorescence)', and the Greek element '-phore' (from 'phorē'/'phoros') where '-phore' meant 'bearer'.

'fluorophore' was coined as a modern scientific term in the 20th century by combining 'fluor-' (from 'fluorescence') and the Greek suffix '-phore'; it entered English technical literature to denote fluorescent groups or dyes and became standard usage in biochemistry and microscopy.

Initially it literally meant 'a bearer of fluorescence' and over time the term has stabilized to mean 'a fluorescent molecule or dye used as a label or probe' in scientific contexts.