Investigations in recent decades have exploited tissue DNA genotyping as a powerful ancillary tool for the precision diagnosis and subclassification of gestational trophoblastic disease. As lesions of gestational origin, the inherited paternal genome, with or without copy number alterations, is the fundamental molecular basis for the diagnostic applications of DNA genotyping. Genotyping is now considered the gold standard in the confirmation and subtyping of sporadic hydatidiform moles. Although a precise diagnosis of partial mole requires DNA genotyping, prognostic stratification according to distinct genetic zygosity in complete moles has recently gained significant clinical relevance for patient care. Beyond hydatidiform moles, DNA genotyping has fundamental applications in the diagnosis or prognostic assessment of gestational trophoblastic tumors, in particular gestational choriocarcinoma. DNA genotyping provides a decisive tool in the separation of gestational trophoblastic neoplasia from non-gestational counterparts/mimics of either germ cell or somatic origin. The FIGO/WHO prognostic scoring scheme requires ascertaining the precise index gestational event and the time interval between the tumor and index gestation, where DNA genotyping can provide highly relevant information. With rapid acquisition of molecular diagnostic capabilities in the clinical practice, DNA genotyping has become closely integrated into the routine diagnostic workup of various forms of gestational trophoblastic disease.