The Permian alkaline lamprophyres from the Spanish Central System (SCS) are highly porphyritic rocks which carry a heterogeneous population of clinopyroxene and kaersutite zoned phernocrysts. Clinopyroxene phenocrysts may show 1) normal zoning (Cpx-I), 2) reverse zoning with Fe-rich green cores (Cpx-II), and 3) reverse zoning with colourless Al-poor, silica-rich cores (Cpx-III). Kaersutite phenocrysts also show a slight reverse zoning. Major and trace element composition of Cpx-I suggests that their compositional variation is related to a crystal fractionation process from melts similar to the host lamprophyres. The Cpx-II cores represent crystallization from highly evolved melts (low Mg-Cr contents and incompatible element enrichment), genetically related with the SCS alkaline magmatism, and the growth or surrounding Mg-rich inner rims points to a magma mixing process. The major and trace element composition of Cpx-III cores supports derivation from a magma which has fractionated plagioclase. This characteristic, together with their similarities when compared to clinopyroxenes from charnockite xenoliths, suggests that they might be xenocrysts from deep calc-alkaline cumulates. The composition of melts in equilibrium with clinopyroxene and amphibole phenocrysts supports a model in which Cpx-II and Cpx-III cores would have been incorporated into a more primitive lamprophyric magma stagnated at lower crustal levels. The low pressure composition of all phenocryst outer rims indicates that they crystallised directly from the host alkaline magma at their subvolcanic emplacement levels.