The objective of this study is to evaluate the morpho-based method (common system) which used to distinguish between zygotic seedling and nucellar seedling of Cleopatra mandarin and Sour orange rootstocks using ISSR technique. Eight ISSR primers were used to check true-to-type of three mother-plants and nine seedlings of two citrus species, Cleopatra mandarin from Giza nursery and Sour orange from Benha nursery. Results showed that ISSR markers were a utility to identify nucellar or zygotic seedlings and check seedlings true to the type of mother plant. Three Cleopatra mandarin seedlings (33.3%) were identified as nucellar seedlings and six seedlings (66.7%) were identified as zygotic seedlings when using ISSR5 primer. While this percentages were different when using ISSR5 primer with Sour orange seedlings, which revealed one of them (11.1%) was identified as a nucellar seedling and eight seedlings (88.8%) were identified as zygotic seedlings. This suggested that the common method used until now for selection the nucellar seedlings in nursery is not perfect. Finally, that screening of seedlings for early identification of putative zygotic seedlings by ISSR analysis for random and various combinations is essential in citrus to maintain the genetic characteristics of the citrus rootstocks in orchards.