Meningioma is the most common type of primary intracranial tumor. These tumors are typically slow-growing and benign [World Health Organization (WHO) grade 1]. However, 20% of meningiomas (WHO grade 2 and 3) can be difficult to treat owing to their aggressive characteristics and higher recurrence rate, which presents a significant therapeutic challenge. Histopathological grading can yield inconsistent results due to interexaminer variability, which calls for more reliable biomarkers. Genetic and epigenetic alterations may define biological behavior and predict the prognosis of meningioma. The present review highlights the relevant genetic mutations, DNA methylation status in meningioma and their associations with relevant histomorphology, location and prognosis. Mutations in TNF receptor-associated factor 7, Krüppel-like factor 4 (KLF4), v-Akt murine thymoma viral oncogene homolog (AKT1), Smoothened frizzled-class receptor (SMO), Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA), and RNA polymerase II subunit A (POLR2A) were associated with a good prognosis and a low recurrence rate. By contrast, mutations in NF2, TERT promoter, SMARCB1, SMARCE1, CDKN2A/B and BAP1 are associated with poor prognosis and higher recurrence rates. DNA methylation status plays a role in diagnosis, predicting tumor recurrence and prognosis. Combining the WHO grading and molecular biomarkers may lead to better diagnosis, prognosis, and targeted therapy for meningioma.