Abstract Apomictic genera have a complex evolutionary history, including reticulate hybridization, polyploidization and variation in reproduction modes. Restrictions of functional meiosis in polyploid apomictic taxa considerably hamper gene conversion, leaving footprints of past hybridization events in their genomes, which are masked by the homogenization of tandemly organized arrays of nuclear ribosomal DNA in sexual species. Dandelions (Taraxacum) have a highly complex reticulate evolutionary history. Detailed knowledge remains hazy; earlier investigations of rDNA sequences have uncovered the complex pattern derived from evolution but without direct evidence for any particular processes. We investigated the position and number of 45S and 5S rDNA loci in 38 Taraxacum taxa (covering different reproduction modes, geographical regions and putative phylogenetic groups) using fluorescent in situ hybridization (FISH) and measured genome size and GC content. The ITS1-5.8S-ITS2 regions of four sexual and five apomictic taxa were sequenced to investigate inter- and intra-individual variation. Most species considerably differ in the chromosome positions of loci and karyotype patterns, but mostly share the same number of studied loci (45S:5S) in a 1:2 ratio per haploid genome (x = 8), with six exceptions (up to a 4:2 ratio). Genome size (2C) varies sixfold and with GC content partly distinguishes major evolutionary groups. Sexual taxa show limited variation in sequenced regions (with two to eight variants), but apomictic taxa vary significantly (with 20–36 variants). Extensive reticulate evolution in Taraxacum and subsequent phenomena such as genome repatterning and non-effective concerted evolution are probably the cause of the dynamic nature of Taraxacum karyotypes and the large variation in genome size and rDNA sequences.