The present work was conducted during the two successive seasons of 2011/2012 and 2012/2013 at the experimental farm of El-Quassassin Hort. Res. Station, Ismailia Governorate, and Biotechnology Laboratory, Horticulture Research Institute, Agricultural Research Centre, Egypt. The aim of this study was to investigate the effect of three compost fertilizer levels 4, 6 and 8 ton per Fadden using five varieties of bitter fennel on growth, fruits yield and essential oil production of fennel (Foeniculum vulgare Mill).  These varieties were Holland, Indian, Azoricum, German and Local fennel.  Several trails were studied including growth and yield production, biochemical (the essential oil) and molecular genetic (RAPD- and ISSR-PCR) characteristics under Egyptian sandy soil. The results showed that increasing compost level progressively (form 4 to 8 ton/ Fed) and significantly increased the values of such parameters.   Azoricum variety was superior to other varieties under study, as it showed the best growth in terms, fruits yield, fruit essential oil (%) and essential oil production per plant.    The main compounds in all fennel essential oils were: Anethole, Estragole, Fenchone and Limonene. The highest percentage of Anethole found in German variety, while the lowest percentage found in Local variety, where the highest percentage of Estragole (= Methyl chavicol ) compound undesirable found in Local variety, while the lowest percentage found in Holland and German  varieties.    Random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat (ISSR) molecular fingerprinting markers were employed as genetic markers for the assay of the genetic relationship of five fennel varieties.        In RAPD analysis, 10 selected primers displayed a total of 98 amplified fragments, in which 60 (61.22%) were polymorphic fragments. Thirty-one out of 98 RAPD-PCR fragments were found to be useful as cultivar-specific markers. The largest number of RAPD-PCR markers was scored for Indian variety (68 markers), while the lowest (49 markers) was scored for Holland variety.    In the meantime, the highest number of RAPD-PCR cultivar-specific markers was generated by primer OP-C04 (7 markers), while the lowest number of RAPD-PCR specific markers (1 markers) was generated by primers OP-A13 and OP-B04.   In ISSR analysis, 4 of the tested ISSR primers generated variable banding patterns. A total of 26 out of 34 ISSR fragments were polymorphic. Eleven DNA amplified fragments were considered as cultivar-specific markers. The varieties distribution on the consensus tree according to the banding patterns of RAPD differed from that based on ISSR. According to the RAPD data, the most two closely related varieties were Indian and Local.  While, according to ISSR results, the most two closely related varieties were Indian and German. This may be due to the possibility that each technique of amplified different parts of the genome. Therefore, it would be useful to use a combination of the banding patterns of the two technique in order to use more segments sites of the genome that verify the validity of the consensus tree.