Inter Simple Sequence Repeat (ISSR) markers were used to assess the genetic diversity among 23 outcross and self pollinated populations of fennel collected from different geographical regions of Iran and some European countries. The experiment was carried out to determine the effect of self-pollination on morphological traits and genetic diversity in the next generation. Fifteen primers produced 248 polymorphic bands with an average of 16.53 fragments per primer in outcross populations, while

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... 7 polymorphic fragments with an average of 14.46 fragments per primer were generated in self-pollinated populations. UPGMA dendrogram using Jaccard's similarity coefficients placed outcross populations in five major groups. The maximum and minimum gene diversity over loci was observed in Albania (0.53) and Poland (0.42) populations, respectively. In general, European fennel populations revealed higher expected heterozygosity (0.47) in comparison with Iranian ones (0.35). Polymorphism Information Content (PIC) ranged from 0.37 to 0.49 in self-pollinated populations, while it varied from 0.39 to 0.46 in out-cross ones. The classification based on morphological data did not confirm the molecular ones in most cases. Self-pollination led to decline in plant height in most of the studied populations. In overall, plant height of the European populations (54-66.02 cm) was less than that of Iranian ones (55-109.54 cm). Self-pollination elevated the yield of essential oil in studied fennels through its influence on fruit set. In conclusion, Albania population had the highest oil content affected by self-pollination; hence, it can be introduced as one of the valued sources in fennel breeding programs aimed for oil yield improvement.