One of the fundamental questions in invasion biology is why an alien species successfully invades one region but fails to do so in another region. In this regard, the recently emerging molecular ecology tools have made it possible to understand the genetic basis of invasion success and/or failure of alien species in different regions. Here we report the results of studies of the population genetic structure and diversity of Parthenium hysterophorus L. – a global plant invader – from two climatically distinct Himalayan regions: Jammu and Kashmir. While P. hysterophorus has successfully invaded across the subtropical Jammu region, it failed to invade the neighbouring temperate Kashmir region. The results, based on the ISSR data, revealed that the populations from Jammu were genetically more diverse than those from Kashmir. This conclusion was further supported by cluster analysis which grouped all the five populations of P. hysterophorus from Jammu region, but clearly separated out the Kashmir population. It is plausible that this low genetic diversity of P. hysterophorus in the latter region, along with the environmental barrier (i.e. temperate climate), has so far prevented the naturalisation and wide spread of this invasive plant species in Kashmir. The research insights from the present study, therefore, have potential implications for understanding the genetic basis of plant invasions.