Polyploidy is a fundamental mechanism in evolution, but is hard to detect in taxa with agmatoploidy or aneuploidy. We tested whether a combination of chromosome counting, microsatellite analyses and flow cytometric measurements represents a suitable approach for the detection of basic chromosome numbers and ploidy in Kobresia (Cyperaceae). Chromosome counting resulted in 2n=64 for Kobresia pygmaea and K.cercostachys, 2n=58 and 64 for K.myosuroides, and 2n=72 for K.simpliciuscula. We characterized eight microsatellite loci for K.pygmaea, which gave a maximum of four alleles per individual. Cross-species amplification was tested in 26 congeneric species and, on average, six of eight loci amplified successfully. Using flow cytometry, we confirmed tetraploidy in K.pygmaea. Basic chromosome numbers and ploidy were inferred from chromosome counts and the maximum number of alleles per locus. We consider the basic numbers as x=16 and 18, with irregularities derived from agmatoploidy and aneuploidy. Across all Kobresia taxa, ploidy ranged from diploid up to heptaploid. The combination of chromosome counts and microsatellite analyses is an ideal method for the determination of basic chromosome numbers and for inferring ploidy, and flow cytometry is a suitable tool for the identification of deviating cytotypes.