Rhaponticoides iconiensis (Hub.-Mor.) M. V. Agab and Greuter is a rare and endangered endemic species of the Konya region of Turkey. One related taxon, Rhaponticoides mykalea (Hub.-Mor.) M. V. Agab and Greuter, is morphologically similar but occurs in different geographical locations. This study has been conducted on the biology of this threatened plant in order to understand better the factors that should be included in the development of conservation practices. The genetic variations were studied using RAPD markers and SDS-PAGE profiles of total seed proteins for three R. iconiensis populations and two R. mykalea populations. The analyzed R. iconiensis populations belonged to different soil types (calcareous and volcanic). The analyzed R. iconiensis and R. mykalea populations belonged to different bioclimatic zones. A genetic diversity within populations was detected both by SDS-PAGE and RAPD for R. iconiensis populations. The level of variation did not differ with respect to soil type for the species studied. Populations collected from the same soil types carried more polymorphisms than those grown in different zones. The genetic diversity was revealed more clearly for all populations by RAPD than through analyzing proteins. Differentiation between ecological groups was higher than that revealed within groups. Conservation programs should take into account the level of genetic diversity within population revealed by these markers according to soil types.