The Austral papaya (Vasconcellea chilensis) is an endangered species that has valuable characteristics for introgression into other papaya species. These characteristics include disease resistance, cold tolerance and latex with low proteolytic activity. It is a species that grows under extreme environmental conditions of drought, salinity and temperature; it is found growing naturally in Chile but today only as three remnant populations. The results presented here, using inter simple sequence repeat molecular markers, along with morphological trait analyses, suggest that these relict populations are the result of a relatively recent fragmentation. This implies that the fragmentation has not yet had its full effect on the genetic variation and so emphasises the need for clear and urgent conservation measures to preserve the remaining genetic variation, particularly for the most northern of the three populations which is presently unprotected.