The objective of this study was to differentiate between five rabbit breeds at four microsatellite loci on autosomal chromosomes 5, 7 and 19, and to assess the association between detected microsatellite alleles and some economical traits. The breeds were Baladi White (BWH) and Baladi Red (BR) as native Egyptian breeds, and New Zealand White (NZW), American Rex (AR) and Chinchilla (CH) as exogenous breeds. Genomic DNA was extracted from nine individuals/breed, and screened by four pairs of microsatellite markers (Sat5, D7Utr4A, D7Utr4B and D19Utr4B). A total of 26 alleles was detected, with an average of 6.5 alleles per locus. The within-breed genomic variability was in general high, and was not significantly differed between breeds. The expected heterozygosity was also high and ranged from 0.769 in NZW to 0.826 in CH, with no significant differences between the breeds. The average polymorphism information content (PIC) varied from 0.286 in BWH to 0.593 in CH. The genetic distance indices revealed close genetic relationship between BWH and CH and averaged 2.629, however the genetic distance between AR and NZW averaged 3.355. Many alleles were found to associate many growth and reproduction traits. D7utr4A`4 showed significant association with body weight and chest circumference at 8 weeks of age and body length at 8 and 10 weeks of age. The microsatellite locus D7Utr4B on chromosome 7 showed significant association with parity.