Fennel is an open-pollinating medicinal crop that needs to be pollinated by insects such as bees to have maximum fruit and oil yield. This may limit fruit production in the absence of insect pollinators. In order to examine the possibility of the plant evolution to self-pollination, using partially self-compatible ecotypes, eight populations of self and bee-pollinated fennel each consisted of 9 plant genotypes forming a final collection of 72 contrasting lines were field evaluated in two years. Averaged over all plant genotypes and populations, progenies derived from selfing had 20.86 and 3.58 % less fruit yield than those derived from bee pollination in two consecutive years mainly due to the depression in the number of effective umbels per plant as the main yield component. Multivariate data analysis differentiated self- and open-pollinated populations; however, this discrimination and inbreeding depression were significantly high only at the year of establishment in this perennial herb. Also, inbreeding depression was not observed for fruit yield, yield components and essential oil content in some of the genotypes within the populations with no or minimum genotype*year interaction. This suggested that it is possible to utilize self-pollination in developing environmentally stable productive pure line varieties with possibly modified essential oil content applicable for future genetic improvement of fennel.