An aneupolyhaploid (2n = 36) of the decaploid Thinopyrum ponticum and an amphidiploid (2n = 28) of Hordeum violaceum x Hordeum bogdanii were produced through anther and inflorescence culture, respectively. Meiotic associations in pollen mother cells at metaphase I of these plants were analyzed. The aneupolyhaploid arose by direct embryogenesis from a microspore without passing through a callus phase. The mean pairing frequencies of 2.67 univalents (+) 0.54 rod bivalents (+) 8.85 ring bivalents (+) 2.75 trivalents (+) 0.17 chain quadrivalents (+) 0.56 ring quadrivalents (+) 0.65 pentavalents in the aneupolyhaploid (2n = 36) best fit the 2∶2∶1 model. However, the frequent multivalents (up to five trivalents, or three quadrivalents, or four pentavalents in a cell) indicated that decaploid T. ponticum has five sets of closely related genomes representable by the genome formula J1 J1 J1 J2 J2. Colchicine treatment of inflorescence-derived H. violaceum x H. bogdanii regenerants greatly enhanced the rate of chromosome doubling, and completely doubled regenerants could be isolated. The H. violaceum x H. bogdanii amphidiploid had a mean pairing pattern of 12.53 univalents (+) 5.57 rod bivalents (+) 1.97 ring bivalents (+) 0.07 trivalents (+) 0.03 hexavalents, indicating the presence of desynaptic gene(s) in the original diploiid hybrid. Therefore, the pairing frequency in that diploid hybrid was an under-estimate of chromosome homology between the parental genomes, and additional diploid hybrids are needed to assess the genome homology between H. violaceum and H. bogdanii. These two contrasting experiments demonstrated that tissue culture techniques are useful in altering the ploidy level to produce plant materials suitable for genome analysis and phylogenetic studies.