Gender identification is essential in forensic science to provide the initial information for criminal investigation. However, gender identification by amplification of amelogenin gene sometimes showed controversial cases, in which male samples was falsely identified as females and female samples was recorded as males. We reported the anomalous amelogenin results of 2 male samples (out of 238 males) represented as females (Y deletions) and another 2 samples with (X deletions) in Benghazi (Libya). The frequency in both was about 0.8. Higher than those of the other populations reported.To confirm amelogenin results of the 2 controversial samples, DNA was further used in SRY and Y-STR typing. All samples typed as males but two showed with X chromosomes. From the results, it was highly suggested that for the controversial cases of human gender identification with amelogenin tests, amplification of SRY gene or/and Y-STR markers will be adopted to confirm the gender.