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We examined rock–soil–plant relationships of three endemic Cactaceae species [Cephalocereus apicicephalium E.Y. Dawson, C. nizandensis (Bravo & T. MacDoug.) Buxb., and C. totolapensis (Bravo & T. MacDoug.) Buxb.] from the tropical deciduous forest of the Tehuantepec River basin, Mexico. The goal was to explain the relationships between the species, rock, soil, and calcium oxalate. The x‐ray diffraction patterns from the rock and soil analyses showed that the species do not share either a rock or a soil type. Cephalocereus apicicephalium grew exclusively on outcrops of limestone with quartz on the summit to backslope of the hill and C. nizandensis grew in metalimestone outcrops on the summit and shoulder of the hill, while C. totolapensis preferred acid soils from andesite, growing also on siltstones or on mica schist on the shoulder to toeslope of the hill. Although only insignificant quantities of soluble Ca were found in the soil, weddellite is abundant in the plant tissue. This suggests that the plants take up the Ca they need and that weddellite is a genetically fixed characteristic related to deflection of excess radiation or an herbivore deterrent. Energy dispersive x‐ray analysis showed that calcium oxalate crystals contained other elements (Si, Mg, Na, K, Cl, and Fe) and that these impurities modified the crystal shape, as for bipyramids in C. totolapensis Biominerals did not change the mineral composition of the soil. The three species are distributed as edaphic or rocky islands, giving rise to their allopatric and patchy distribution across the landscape. Finally, the endemicity of the three Cephalocereus species is promoted by the parent material and the particular soil conditions in the area in which each one grows.

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