Morphological characters and karyotype of three populations of Allium caeruleum Pallas distributed in Xinjiang, China, were studied. The results showed that there were morphological and karyotypic differentiations in different populations of A. caeruleum Pallas. There were no morphological differences in 43 characters of three populations such as bulb, plant type and leaf shape. There were significant differences or highly significant differences in 19 characters of three populations such as bulbil, leaf colour, leaf length, individual leaf number, flower number, umbel height and scape length. The karyotype formula was 2n = 2x = 16 = 12m + 4sm for A. caeruleum Pallas (Urumqi population).The karyotype formula was 2n = 3x = 24 = 18m + 3sm + 3st for A. caeruleum Pallas (Tacheng population) .The karyotype formula was 2n = 4x = 32 = 28m(4SAT) + 4sm for A. caeruleum Pallas (Yumin population). Morphological and karyotype differentiation were found in three populations of A. caeruleum Pallas, and the ploidy levels was diploid, triploid and tetraploid, respectively. However, morphological characters and ploidy levels were stable within populations. The composition and relative length of chromosome of three populations of A. caeruleum Pallas are different. The karyotypes of them are 2A types.