Basal hyphae thin- to slightly thick-walled, 3-5(-6) µm wide, with rather small clamps. Echinocysts sessile or stalked, hyaline, globose to ellipsoid or ovoid, 6-11 X 6-8 µm, strongly cyanophilous, with a basal clamp, apically with 4-8 slender, tortuous "flagella" up to 8 µm long. Cystidia hyaline, thin-walled, clavate to generally cylindrical and constricted below the apex, thus becoming capitate, 28-40 X 5-6.5 µm. apex up to 8 µm wide, constriction 2.4-4 µm wide. Basidia clavate to typically urniform, 30-50 X 7-9(-10) µm, with four sterigmata. Spores hyaline, thin-walled, ellipsoid to subcylindrical, (7-)8-10(-10.5) X (4-)4.5-5(-6) X (4.5-)5-6(-6.5) µm, smooth, not amyloid.

The species is very close to Hyphoderma comptum (H. S. Jacks.) Jülich, which has similar, but significantly smaller structures. Stephanocysts, echinocysts, and small vesicles are considered to be homologous; they are all strongly cyanophilous, have a basal clamp directly under the swelling, and are found in the subiculum only. Moreover, in H. flagellatum both vesicles with flagella (echinocysts) and similar vesicles without flagella are present. Species with these structures generally also have cystidia with a constriction directly below the apex; they are considered to be closely related. To this group belong: H. comptum, H. echinocystis J. Erikss. & Strid, H. flagellatum and H. praetermissum (P. Karst.) J. Erikss. & Strid.