Our goal for this study to characterize three species germplasm of family Apiaceae, namely (cumin, caraway and coriander), to make a chromosome characterization and molecular fingerprint for the mentioned species. Results performed on Karyomorphological showed that; Cuminum cyminum L. (cumin: 2n=14), Carum carvi (caraway: 2n=20) and Coriandrum sativum (coriander: 2n=22). The total Chromatin Relative Length percentage (RL%) showed cumin ± 10.69 μm ± 19.70 μm, caraway ± 7.30 μm ± 13.40 μm and coriander ± 5.58 μm ± 12.07 μm. Satellites in all the cases were associated to short arms. The molecular characterization for the three species (caraway, cumin, and coriander) was conducted using 5 AFLP combinations and 15 anchored-ISSR primers. The total amplified bands were 330 (162 ISSR+168 AFLP), with an average 83.75% (89.5 ISSR+78 AFLP) per primer. The combined dendrogram based on both AFLP and SSR markers for the three accessions was divided into 2 main clusters; the first cluster has 2 accessions (caraway and cumin) with 60% similarity, while coriander falls in a distinct cluster.