In this book we present a study aimed to determine the morphological, biochemical (protein SDS-PAGE and isozyme) and molecular (RAPD- and ISSR-PCR) characteristics in different ecological types of milk thistle collected from Egyptian habitats and identify levels of active ingredients as a way towards improvement of this plant on the commercial leve. the results of SDS-PAGE data for twelve silybum accessions confirmed that there were negative markers. Also, the results of RAPD and ISSR-PCR data analysis confirm that there were two positive markers. Finally both positive and negative marker for the highest production of the fixed oil by primers HB12 and X06 and three positive markers the lowest production of the fixed oil by primers HB14 and HB15.