In order to evaluate molecular and phenotypic diversity and detecting molecular markers for six summer squash inbred lines belong to species [Cucurbita   pepo L.], five RAPD and five ISSR primers were used as well as 12 economical traits were estimated. These primers succeeded in generating reproducible and reliable amplicons. RAPD revealed 88.1 % of polymorphism while ISSR techniques showed 80.5% polymorphism. The resolving power (Rp) value for RAPD technique was 5.00 which was higher than 3.40 of ISSR technique. Therefore, the RAPD technique was better than ISSR technique in evaluated molecular diversity and discrimination capacity among lines. But, the ISSR technique was better than RAPD technique in showing unique markers (21 for ISSRs and 9 for RAPDs). Also, the correlation between phenotypic distance (PD) and molecular distance (MD) based on ISSRs was 0.173 highest than with MD based on RAPDs (0.045). On the other hand, with the exception of P6 which gave significant desirable value in two traits (number of fruits and yield per plant), each of the other five strains gave a significant desirable value in one trait, thus the number of these traits which  distinguished in the six inbred lines were 7 traits. These traits could be linked with all unique markers detected in this study. The inbred line P5 showed the highest number of unique markers (10, 9 of them were  positive), one or some of which may be linked with NL trait that showed in this inbred line a significant desirable value. Followed by the inbred line P6 which showed seven unique markers (six of them were positive) one or some of which may be linked with NF and/or Y/P traits. This indicated that some of these markers may be used as markers assisting selection in the breeding and improvement of squash.