Hibiscus (Family Malvaceae), is an evergreen flowering shrub native to East Asia. It is widely grown as an ornamental plant throughout the tropics and subtropics. The flowers are large, generally red in the original varieties, firm and lack any scent. Numerous varieties, cultivar and hybrids are available with flower colors ranging from white through yellow and orange to scarlet and shades of pink with both single and double sets of petals.  Consequently, a greet attention has been focused on hibiscus. On the other hand, isozymes considered to be powerful tool for gene variability. Therefore an attempt was done to estimate peroxidase isozymes activities in five varieties of Hibiscus taken from Antoniades Botanical Gardens, Alexandria. Egypt., and classified as four varieties 1- Athene, 2- Cairo, 3- President, and 4- Saphire for species Hibiscus rosa-sinensis and Red variety for species Hibiscus mutabilis . Such a trait of activity of peroxidase was used in the five varieties under study to regulate genetic diversity.  The result obtained showed that there were a similarity of peroxidase isozymes activities in varieties 1- Athene, 2- Cairo, 3- President, and 4- Sapphire and in contrast, the activities of peroxidase isozymes found to be different in the variety Red since it was found to be more active. The same result observed on genetic diversity since it showed two clusters. Cluster 1 includes four varieties 1- Athene, 2- Cairo, 3- President, and 4- Saphire while cluster 2 includes variety Red.  The importance of such data in the breeding programs is to develop an index for parental selection and the hybridization between different cluster varieties expected to increase the hybrid vigor which can be used in breeding programs.