Plants unbranched, protruding relatively little above soil. Roots obconic taproots; secondary roots diffuse. Stems top-shaped, flat-topped (aerial part sometimes hemispheric in old age or in dense subtropical vegetation), protruding above ground 0-2 × (4-)7.5-15 cm, firm; tubercles 9-15(-20) × 3-7 mm; axils with short wool, bristles absent; cortex and pith not mucilaginous; latex abundant in healthy tissue throughout cortex of stem, tubercles, and sometimes flower receptacle, sticky, white. Spines (8-)10-18(-27) per areole, usually brownish, darker at tip, glabrous; radial spines (8-)10-22(-26) per areole, white to white-and-brown or brown , needlelike, 6-15(-16) mm, stiff, abaxial spines longest; central spines (0-)1(-4) per areole, porrect or ascending, not hooked, (0.5-)2-8 × 0.15-0.45 mm; subcentral spines 0. Flowers 1.9-3.8 × 1.5-3 cm; outermost tepal margins entire; inner tepals white, greenish or cream to pale pink, with tan, pink, greenish, or brownish midstripes, 11-19 × 2-2.5 mm; stigma lobes externally green, internally green or red (or pink), 2.5-3 mm. Fruits brilliant red: scarlet, carmine, or crimson, obovoid to clavate, 10-35(-40) × 5-8 mm, juicy only in fruit walls; floral remnant weakly persistent. Seeds reddish brown, sometimes yellowish when fresh, 1-1.2 mm, deeply pitted; testa thin, relatively flexible; anticlinal cell walls sinuate, interstices narrower than pit diameters; pits cavernous or deeply concave. 2n = 22. Green fruits of Mammillaria heyderi with fully mature, viable seeds precede the ripe (elongate) fruits by six months to a year.

Plant: Low globular cactus < 10 cm with milky sap; stem solitary, noticeably sunken on top, wider than tall; axils initially woolly; flowers mostly cream, forming a circle around stem below the apex.