• Achnanthes elliptica var. exigua Cleve-Euler, 1953 (uncertain > unassessed)
• Achnanthes exigua Grunow, 1880
• Achnanthes exigua f. angustirostrata Krasske, 1939 (uncertain > unassessed)
• Achnanthes exigua f. aperta Guermeur, 1954 (uncertain > unassessed)
• Achnanthes exigua f. heterovalvata Krasske, 1923 (uncertain > unassessed)
• Achnanthes exigua f. profunda Manguin, 1954 (uncertain > unassessed)
• Achnanthes exigua f. semiaperta Guermeur, 1954 (uncertain > unassessed)
• Achnanthes exigua f. subcapitata Suxena & Venkateswarlu, 1968 (uncertain > unassessed)
• Achnanthes exigua f. subglobosa Manguin in Bourrelly & Manguin, 1952 (uncertain > unassessed)
• Achnanthes exigua f. subglobulosa ‘Manguin' according to Guermeur, 1954 (uncertain > unassessed)
• Achnanthes exigua var. angustirostrata (Krasske) Lange-Bertalot in Lange-Bertalot & Krammer, 1989 accepted as Achnanthes exigua f. angustirostrata Krasske, 1939
• Achnanthes exigua var. baikalensis Skvortzow, 1937 (uncertain > unassessed)
• Achnanthes exigua var. baikalensis f. capitata Skvortzov (uncertain)
• Achnanthes exigua var. capitata Amossé, 1921 (uncertain > unassessed)
• Achnanthes exigua var. capitata Hustedt, 1934 (uncertain > unassessed)
• Achnanthes exigua var. constricta (Grunow) Hustedt, 1921 accepted as Achnanthes exigua Grunow, 1880
• Achnanthes exigua var. constricta (Torka) Hustedt, 1930 accepted as Cocconeis exigua var. constricta Torka, 1909
• Achnanthes exigua var. elliptica Hustedt, 1937 (uncertain > unassessed)
• Achnanthes exigua var. exigua Grunow in Cleve & Grunow, 1880 (uncertain > unassessed)
• Achnanthes exigua var. exigua Pantocsek, 1902 (uncertain > unassessed)
• Achnanthes exigua var. globulosa Guermeur, 1954 (uncertain > unassessed)
• Achnanthes exigua var. heterovalva Krasske, 1923 accepted as Achnanthidium exiguum var. heterovalvum (G.Krasske) D.B.Czarnecki, 1994 accepted as Achnanthes exigua f. heterovalvata Krasske, 1923
• Achnanthes exigua var. indica Skvortzow, 1935 (uncertain > unassessed)
• Achnanthes exigua var. nipponica Skvortzow, 1936 (uncertain > unassessed)
• Achnanthes exigua var. rhombica Skvortzov, 2012 (uncertain)
• Achnanthes exigua var. siamense Hirano, 1967 (uncertain > unassessed)
• Achnanthes exigua var. staurophora Pantocsek, 1905 (uncertain > unassessed)
• Achnanthes exigua var. tenuirostrata Guermeur, 1954 (uncertain > unassessed)
• Achnanthes exigua var. typica Cleve-Euler, 1953 (uncertain > unassessed)
• Achnanthes exigua var. undulata Frenguelli, 1953 (uncertain > unassessed)
• Achnanthes exigua var. yabeana Skvortzov (uncertain)
• Achnanthes exigua var. yabeana Skvortzow & Noda, 1971 (uncertain > unassessed)