Fritillaria japonica is characterised by the presence of a distinctly divided style, having smooth tepal margins and nectaries and white anthers.

[1] He provides the following description (in Latin)[a] — "Stem 5 thumb breadths, arising from a bulb of few scales and scarcely larger than a pea, with 4–5 leaves at its apex, lanceolate and tapering to a point at both ends; single nodding spreading-campanulate flower born on a pedicel; perigonium half a thumb breadth, pointed and recurved at the tip, the outside pale lilac and dotted, the inside dotted lemon yellow and blood red; anthers yellow and elliptical-oblong; stigma with three linear lobes."

He ends with Ad iconem libri iaponici determinavi, alluding to the fact he had examined the illustration in Iinuma's Somoku-zusetsubook (1856).

When Baker (1874) divided Fritillaria into subgenera, he was unsure where to place F. japonica and listed it under Species dubiae.

[8] It was not till 2001 that Rix placed all the endemic species of Japan into one subgenus, Japonica,[9] a decision subsequently validated by molecular phylogenetic analysis.