Lilium is one of the six major bulbous genera crops and also one of the leading cut flowers all over the world. It has three important markets: fresh-cut flowers, potted flowering plants and bulbs for domestic gardens and formal landscapes. So keeping in view the importance of this ornamental plant, the present study was conducted to induce mutation (in vivo and in vitro mutagenesis) in different cultivars of Lilium to get the new varieties having better morphological traits including plant height, leaf and flower size, flower shape and flower colour. For this purpose an efficient protocol has been optimized for micropropagation of ten cultivars present in four major groups (Oriental, Oriental x Trumpet, Longiflorum x Oriental and Longiflorum) of Lilium to get the shoots that were further used as plant material for in vitro mutagenesis. MS medium fortified with BAP 0.1 + Kin 0.1 + IAA 3.0 (mg/L) has been found to be best for shoot initiation. Effect of shaking cultures and sucrose concentration was also observed in the present study. It was observed that cultures inoculated in the same medium but in agitation position with 120 (rpm) showed higher regenerated frequency as compared to stationary cultures. Similarly moderate sucrose concentration (60 g/L) proved to be better as compared to 30 and 90 (g/L). Healthy regenerated plantlets were acclimatized in sterile mixture of sand, soil and cocopeat in the ratio of 1:1:1. Mutagenesis was induced in all the groups of Lilium including by treating the bulbs (in vivo mutagenesis) and regenerated shoots (in vitro mutagenesis) through plant tissue culture during the first phase of current study with different doses of gamma rays 2.0-10.0 (Gy). It was noticed that growth of plants in both in vivo and in vitro mutagenesis was affected by gamma rays. Except in Samur La pink cultivar of Lilium, higher doses have inhibitory effect on plant growth, but in Samur La pink of Oriental group of Lilium, stimulatory effect was observed at higher doses of gamma rays. Superior mutants were selected on the basis of change in flower morphology. Larger flowers with smooth petals were obtained at 10.0 (Gy) dose of gamma irradiation. Similarly changes in flower morphology were also noticed in Montezuma-O-red, Advantage La salmon, Golden tycon yellow and Easter lily cultivars of Lilium at different gamma irradiation doses. It is evident from the results of present investigation that mutagenesis combined with plant tissue technique lead to varietal improvement of different cultivars of Lilium. Further study was also carried out to make the molecular characterization of control and mutants of same cultivar to detect the genetic polymorphism and variations. Two different molecular marker systems including Random Amplified Polymorphic DNA (RAPDs) and Simple Sequence Repeats (SSRs) were selected for the purpose. Among the molecular markers, Randomly Amplified Polymorphic DNA (RAPDs) was used as a marker of choice in the present investigation. It was noticed that mutagenesis caused changes at genetic level and separated the control genotypes from the irradiated ones into different groups depending on the genetic variation occurred at different doses. Mostly control and mutants treated at lower doses of gamma rays were combined in one group while genotypes treated at higher doses were separated in another group. Other molecular marker system selected for the present investigations was Simple Sequence Repeats (SSRs) due to high level of polymorphism and reliability. Genetic polymorphism along with the respective allele sizes, PIC (Polymorphic Information Content) values and Hobs (Observed heterozygosity) of the cultivars was also recorded. These markers also separated the control and mutant genotypes on the basis of doses of gamma rays like RAPDs. It is evident from the above results that mutagenesis (in vivo and in vitro) caused genetic variations proved by RAPDs and SSRs which lead to production of new varieties having improved morphological traits.