Fennel ( Foeniculum vulgare Mill) belongs to Apiaceae family and is one of the oldest medicinal plants in Iran. It is a perennial species which is widely used in food, medicine, and cosmetic industries. It has originated from Mediterranean and southern Europe countries. The present research was conducted to determine genetic variation of eighteen collected accession of fennel from different parts of Iran and two exotic accessions using morphological and molecular traits. Genotypes were planted in the field according to a completely randomized block design in three replicates and studied for two agronomic years (2011-2012). Data were combined for the two years, and then statistical analysis was preformed for each year separately.Results of analysis of variance for both years indicated a wide variation for most of studied traits. An accession from Isfahan plus one from Tabriz had the highest grain yield per plant in first and second agronomic years. Broad sense heritability for the studied traits was estimated to range as moderate to high for both years. Path analysis indicated that there was a significant genotype*environment interaction for all traits except for the one thousand grain weight and grain width. Evaluation of traits correlation coefficient indicated that days to 50% flowering, days to 50% ripening, days to 90% ripening and the number of fertile umbels in the first agronomic year and number of fertile umbels, inflorescence diameter and one thousand grain weight in the second year had high and significant correlation to grain yield per plant. Results of stepwise regression for both years showed that umbels heights and numbers had the greatest contributions to account for grain yield variations per plant. Also results of path analysis emphasized the important role of these traits on grain yield per plant. Results obtained from factorial analysis and cluster analysis confirmed high variation among studied accessions for each individual year. Since the studied traits were quantitative and highly influenced by environment, presence of significant difference in statistical parameters between the two years was expected. The eight ISSR primer pairs used amplified a total of 64 DNA bands among samples from which, 62 bands (97%) were polymorphic.
