Two granitic pegmatites with mixed (NYF + LCT) signatures from the Moldanubian Zone, Czech Republic, were examined to determine their origin. On the basis of geological setting, paragenesis, geochemical modeling and chemical composition of rocks and minerals, two contrasting modes of origin were discerned. The Li-bearing (lithium micas + elbaite) Kracovice pegmatite, with “amazonite”, samarskite and fergusonite, is the product of the strong fractionation of pegmatite-forming melt derived from the orogenic I-type Třebíč pluton. Geological, petrological, compositional and isotopic data from this ultrapotassic melasyenite–melagranite point to mixing of a mantle-derived magma with (leuco)granitic melt from crustal rocks. The granite–pegmatite system of the Třebíč pluton and the mainly Li-bearing Kracovice pegmatite are typical examples of the mixed (NYF + LCT) petrogenetic family. The contaminated elbaite-subtype pegmatite Bližná I, Český Krumlov Unit, with lithium tourmalines (elbaite, liddicoatite, uvite), primary REE minerals [bastnäsite-(Ce), parisite-(Ce), allanite-(Ce)] and Ca(Mg)-rich minerals (diopside, uvite, titanite), gained its mixed signature through a unique pre-emplacement process involving the external contamination with Ca, Mg and REE of an evolved (LCT) pegmatite-forming melt by distal carbonatite-like marbles with an NYF signature. Despite the clearly mixed-signature mineralogy and geochemistry, the Bližná I pegmatite represents a special type of contaminated LCT pegmatite rather than a member of the mixed family.