AlliumhookeriThwaites belongs toAmaryllidaceae family is one of the most important medicinal plants, enormously used in cancer or inflammation because it contains large amounts of sulfonylmethane.It is also used to treat coughs, colds, fatigue and to recover immunity. Karyotypic study showed that somatic chromosome number is 2n = 22. Only nearly sub median and nearly median chromosomes are found in the complement. Karyotype formula = 1 nsm(-)+ 10 nm=2n=22. The total length of long arms is 60.36 µm, ranging from 3.16µm to 8.23µm. Total length of short arms is 31.57µm, ranging from 1.75µm to 4.11µm. The total length of the chromosome is 92.17µm, ranging from 4.78µm to 12.35µm. Relative chromosome length ranges from38.70µm to 100 µm. Arm ratio ranges from1.70 to2.38.Tf %= 41.63.Centromeric index ranges from 0.40 to 0.28 and The total chromatin index is 100, ranging from 5.18 to 13.40. Anomocytic type of stomata is observedStomatal index and stomatal size were calculated. The maximum length (53.6±2.06µm) was observed in basal portion of the adaxial surface and the minimum length (45.2 ± 1.40µm) was observed in the middle portion of abaxial surface. The maximum width size (24.8±1.11µm) was observed in the basal portion of the adaxial surface and the minimum width was (18.8 ± 1.14µm) at the middle portion of the abaxial surface. Stomatal index 12.63±0.5) maximum and minimum (6.13±0.40) was observed.