This study was undertaken to evaluate the field performance of the two newly promising bred eggplant F1 hybrids (H1 and H2) relative to a commercial eggplant hybrid (Alabaster, C4) as a reference, as well as apply a dependable DNA fingerprinting technique (PCR-based, Inter Simple Sequence Repeat, ISSR markers) for identification and documentation of locally produced eggplant F1 hybrids. Vegetative growth and yield parameters for H1, H2, and C4 eggplant hybrids were evaluated under four ecological conditions and in different geographic governorate locations (Giza “L-1", Menofia “L-2", Qalyubia “L-3" and El-Behaira “L-4") during the two growing seasons of 2020 and 2021 The means of locally produced eggplant F1 hybrids (H1 and H2) exceeded or equaled the means of the reference hybrid (C4), especially under the conditions of Qalyubia (L3) and Giza (L1) for the characteristics of plant height, number of branches/plant, number of leaves/plant, early flowering, early fruit yield, total fruit yield, number of fruits/plant and the average fruit weight. Furthermore, nineteen ISSR primers were used to identify the genetic fingerprint of the above-mentioned hybrids (H1, H2 and C4) in addition to two local parental lines (P1 and P2). ISSR analysis revealed 243 distinct DNA amplified bands with polymorphic bands of 50.21%. The percentage of polymorphism ranged between 9% and 88% with an average level of 50%. The PIC value varied from 0.09 to 0.49 with an average of 0.36. Seven ISSR primers (HB12, 17899-A, UBC-844, UBC-892, UBC-895, ISSR-59 and ISSR-DAT) produced distinctive fingerprints associated with H1 hybrid. In the same context, eight primers (HB10, HB12, UBC-892, UBC-808, ISSR-55, ISSR-01, ISSR-59 and ISSR-DAT) were distinctive for H2 hybrid. While the commercial hybrid “C4" was distinguished by only three primers (UBC-850, UBC-881 and ISSR-9). The highest similarity value of 0.89 was found between P1 and H1, while the lowest value of 0.78 between P1 and H2. It may be concluded that local eggplant hybrids (H1 and H2) performed superiorly in most studied traits and displayed more polymorphisms than the commercial eggplant hybrid “C4".