Genetic diversity changes in cotton have been studied using different molecular markers, but little is known about the impact of plant breeding on the cotton genome. The objective of the present study was to assess diversity changes in Egyptian cotton varieties released from 1920 to 1998 using 19 RAPD markers. The total number of fragments ranged from 65 to 90 with an average 82.8. Fragment frequency ranged from 0.157 to 0.217 with an average of 0.20. The number of private fragments ranged from one to six. These results suggest that the Egyptian cotton breeding has reduced genetic diversity in the cotton genome. The Shanon information index ranged from 0.125 to 0.209 with an average of 0.147. The expected heterozygosity values ranged from 0.086 to 0.143. The Nei genetic distance among the five released periods based on RAPD markers ranged from 0.099 to 0.269 with an average 0.164. The five cotton breeding periods were classified into four major groups. The PCOA1 and PCOA2 axis explained a reasonable amount of variation 41.68% and 74.04%, respectively. A significant correlation coefficient between gene diversity and the number of fragments was high, r = 0.985 (P > 0.01). Furthermore, analysis of AMOVA revealed non-significant genetic variance among breeding periods. The proportion of RAPD variation accounted by decadal grouping was low (Φ_PT = 0.066, p = 0.230). A genetic shift was observed in the cotton varieties released over the five breeding periods. These results illustrate the impact of the cotton breeding on the Egyptian cotton genome.