Male pseudohermaphroditism is a rare disorders of sex development (DSD) that is manifested by a female-like appearance or incompletely differentiated external genitalia in an individual with a Y chromosome. In this paper, we report our investigation of the case of a 33-year-old Chinese female who was diagnosed with a malignant mixed germ-cell tumor of the ovary. To confirm the sex of the female, we utilized genetic approaches to detect amelogenin and Y-STR loci. Y chromosome microdeletion was performed to identify existing deletions in the AZF regions and SRY. Chromosome karyotyping and whole-exome sequencing (WES) were then applied to reveal the deletion of sex chromosome segments and pathogenic variations in DNA sequences. Using DNA-STR genotyping, we detected both AMEL-X and AMEL-Y fragments. We also found haplotype Y-STR loci and detected all alleles. Furthermore, no microdeletion was detected in the AZF regions and SRY. The chromosome karyotyping was 46, XY. WES revealed a transversion mutation of 58T → C in the androgen receptor exon 1, which could be the pathogenic variant in this case of abnormal sexual development. Sex determination in forensic DNA typing is based on the amelogenin system. It is important that forensic biologists should master various genetic approaches to overcome the issue of gender ambiguity caused by DSDs.