Apatite from carbonatites of the Kaiserstuhl complex contains lower Cl, Br, S, Fe, Mn, Th, U and Si contents but higher Sr and Nb contents than apatite from associated alkaline silicate rocks. Apatite from a bergalite sample (carbonate-bearing melilititic dyke rock) and a diatreme breccias (containing both carbonatitic and silicate fragments) shows systematic core-rim and replaced zonations, respectively. The core zone of apatite from bergalite and the relic part of apatite from diatreme breccias have similar compositions as apatite from silicate rocks in terms of Cl, S, Sr and Si contents. In contrast, those for the rim zones of apatite from bergalite and the repaced part of apatite from diatreme breccias are similar to the composition of apatite from carbonatites. These observations imply that a genetic link of alkaline rocks and associated carbonatites in the Kaiserstuhl complex were recorded by the respective apatite compositions.