Sequence-related amplified polymorphism (SRAP) markers were used to detect molecular marker polymorphisms among five parents and four crosses of citrus and their relatives in Aurantioidea. Four SRAP primer combinations produced a total of 160 polymorphic fragments with an average of 40 per primer combination and the an-average polymorphism information content (PIC) of 0.86. The unweighted pair group method arithmetic average (UPGMA) analysis demonstrated that the accessions had a similarity range from 0.35 in the cross between Lemon and Clementine to 0.43 in the Grapefruit parent with a mean of 0.37. The dendrogram separated the parents and the resulted crosses of Citrus species into two main sub-clusters with a similarity value of 0.37. Only one member of the first sub-cluster which is Clementine or the parent of all the resulted crosses. In the second main sub-cluster, Only one member of the first sub-sub-cluster which is Grapefruit or the parent of one cross.  The second sub-sub-cluster has consisted of one parent separated alone (Succari parent) and another sub-cluster. This sub-cluster is formed from the sub-sub-cluster including the parent Cleopatra mandarin and the resulting from cross Cleopatra mandarin x Clementine. The last sub-cluster has consisted of one group containing the parent Lemon and the resulted cross Lemon x Clementine. The other group consisted of two crosses; Grapefruit x Clementine and Succari x Clementine.