Two human skulls were found during basement construction from November 30th, 2016, to December 1st, 2016, in Balai Pemuda, Surabaya, one of Indonesia's colonial-era buildings. The discovery of two skulls raised questions, such as the identity and its context of existence. Both skulls were coded as skull 160689 and 160690. This research aimed to reveal the identity of skull 160689 and 160690 based on the positive identification procedure of forensic anthropology. This research applies the method of the forensic anthropology identification procedure. This method was used sequentially, firstly age, secondly gender, thirdly population affiliation, fourthly stature, and lastly, individual characteristics. Interestingly, the individual characteristics of skull 160690 have distinct evidence for explaining its identity, for instance, dental modification, disease markers, and asymmetrical head shape. Based on the positive identification results on skull 160689 and 160690 showed both skulls were female and affiliated with Mongoloid population. At last, individual characteristics and deformation on the occipital area were indicated as an unintentional deformation caused by pressure continuously on the left side of the occipital area. Plagiocephaly could be a result of incorrect sleeping position during childhood.