Five tomato inbred lines (Solanum lycopersicum L.,) obtained from five widespread varieties in Egypt were used in this study to assess genetic diversity among them. Seven RAPD and six ISSR primers were succeeded in generating reproducible and reliable amplicons. Although, the RAPD technique was better than ISSR technique in assessment for molecular diversity and discrimination capacity among lines. The Rp value for RAPD technique was 13.7 which was higher than 8.1 of ISSR technique. However, both techniques were suitable tools for detecting reproducible polymorphic patterns and confirmed to be valid in discrimination among lines through the various specific markers of 27 and 18 markers in RAPD and ISSRs, respectively. These markers succeeded in distinguishing each lines and divided them into three groups in cluster analysis with different degrees of MD which ranged from 0.198 to 0.441 with a mean of 0.343. Moreover, 22 various traits estimated for all lines under two different climatic seasons of the summer season of 2014 and the winter season 2015 also which succeeded in description of phenotypic diversity and heterogeneity within lines which divided accordingly into two main groups with different degrees of PD ranged from 0.081 to 0.428 with mean of 0.236. However, insignificant correlations were found among the distances computed based on these two types of genetic diversity as well as, the correlation relationships among these distances and heterosis for most studied traits were not significant. This requires evaluating  genetic diversity for lines which are used as parents in breeding improvement programs of tomato at more than location and under different climatic conditions. Also, through a more number of variable molecular markers and also depending on a more number of  phenotypic traits. Hence, achieving the desired goal from this evaluation, which is the prediction of heterosis for all important traits and which will lead to provision of strenuous efforts to assess hybrids in most breeding programs.