Bulb subglobose to globose, up to 2(-2.5) cm in diameter. Stem up to 70(-110) cm tall, glaucous-green or glaucous purplish green. Leaves 7-12(-14), glaucous-green or purplish green, shallowly canaliculate, linear to narrowly lanceolate, often suberect, all alternate or the uppermost in a whorl of 3, the lower 0.2-1(-1.4) cm broad and (5-)7-10(-15) cm long. Flowers usually 1, rarely 2-3(-4), broadly campanulate to cylindrical, greenish or brownish to dark purplish brown outside, tessellated to obscurely tessellated, sometimes w ith more distinct purplish brown spots, with or without yellowish green fascia, colours paler insi de, segments distinctly upturned at the mouth or not; outer perianth segments ovate-lanceolate, usually acute, 2.2-4(-4.5) × (0.9-)1-1.6 cm; inner perianth segments apiculate or rounded, 1.2-1.9(-2.2) cm broad. Nectaries 0.4-0.6 cm broad and 0.5-0.8(-9) cm long, ovate-lanceolate to broadly ovate, green to brownish green, situated 0.4- 0.5 cm above the tepal base. Filaments up to 1(-1.3) cm, sparsely papillose. Style 1-1.3 cm, 3-fid to 1 / 3 or more than halfway, smooth. Capsule cylindrical, unwinged.
Fritillaria messanensis is a polymorphic species, typically with narrow, usually long leaves, rather broadly campanulate flowers and distinctive, large, broadly ovate (egg-shaped) nectaries, by which it is usually easily distinguishable from its related taxa.