The carnivorous genus Genlisea is characterized by one of the largest genome size differences recorded for Angiosperm genera ranging from half of that of Arabidopsis thaliana to 27-fold larger. This trait, together with the variation of chromosome numbers, makes the genus Genlisea a unique model for studying genome and karyotype evolution. Aiming to describe cytological features, sub-nuclear distribution of methylation marks, chromosome numbers and chromosomal distribution of rDNA were characterized for species of the subgenus Genlisea. Utilizing whole genome sequencing data, a tandem repeat and a retroelement family were demonstrated to be associated with the pericentromeric regions of G. nigrocaulis and G. hispidula, respectively, with an 18-fold genome size difference. Moreover, two novel telomere variants were found replacing the canonical TTTAGG repeat at the chromosome ends of G. hispidula. Furthermore, the majority of chromosomes of three Genlisea species were identified by FISH using chromosome-specific probes. The obtained data provide a basis for comprehensive karyotype evolution studies in Genlisea.