An efficient direct in vitro plant regeneration protocol for Saussurea costus (kuth) was developed using shoot tip explants derived from in vitro grown seedlings to generate genetically uniform plants. Murashige and Skoog (MS) medium supplemented with 1.14 µM thiadiazuron and 2.68 µM naphthalene acetic acid was found to be most optimal for highest for average shoot regeneration (73.33%) with maximum average number of shoots (11.4) and average shoot length (4.17 cm). For in vitro multiplication, shoots cultured on MS medium supplemented with 4.44 µM benzyl adenine, 2.32 µM kinetin and 1.44 µM gibberellic acid were found to grow best with 20.7 average shoot multiplication rate after 5–6 weeks. MS medium supplemented with 2.46 µM indole butyric acid was found to be the best medium for rooting of microshoots (77.78% rooting with 6.0 average number of roots and 3.07 cm average root length). The in vitro raised plantlets were successfully acclimatized under ex vitro conditions. The true to type nature of the in vitro raised plants was confirmed using DNA based ISSR markers for assessment of genetic stability of micropropagated plants. The standardized micropropagation protocol under present study may be tuned towards mass production of roots which are the most economical part of the plant. This would be useful as prerequisite for carrying out any genetic transformation studies while concentrating on any desirable trait in the same herb.