She was a daughter of Stilicho, magister militum of the Western Roman Empire, and Serena. Maria was a sister of Eucherius and Thermantia. "De Consulatu Stilichonis" by Claudian reports that her unnamed paternal grandfather was a cavalry officer under Valens, Emperor of the Eastern Roman Empire. Orosius clarifies that her paternal grandfather was a Romanized Vandal. The fragmentary chronicle of John of Antioch, a 7th century monk tentatively identified with John of the Sedre, Syrian Orthodox Patriarch of Antioch from 641 to 648 calls the grandfather a Scythian, probably following Late Antiquity practice to dub any people inhabiting the Pontic-Caspian steppe as "Scythians", regardless of their language. Jerome calls Stilicho a semibarbarian, which has been interpreted to mean that Maria's unnamed paternal grandmother was a Roman.
The poem "In Praise of Serena" by Claudian and the "Historia Nova" by Zosimus clarify that Maria's maternal grandfather was an elder Honorius, a brother to Theodosius I. Both were sons of Count Theodosius and Thermantia, as clarified in the "Historia Romana" by Paul the Deacon. Genealogists consider it likely that Maria was named after her maternal grandmother, tendatively giving said grandmother the name "Maria".
In c. February, 398, Maria married Honorius, her maternal first cousin, once removed. Her husband was a son of Theodosius I and his first wife Aelia Flaccilla. Honorius was not yet fourteen-years-old. The Epithalamion written in their honor by Claudian survives. He places his flattering description of Maria in the mouth of Venus, a Roman goddess principally associated with love, beauty and fertility, the equivalent of the Greek goddess Aphrodite. "E'en though no ties of blood united thee to the royal house, though thou wert in no way related thereto, yet would thy beauty render thee worthy of a kingdom. What face could rather win a sceptre? What countenance better adorn a palace? Redder than roses thy lips, whiter than the hoar-frost thy neck, cowslips are not more yellow than thine hair, fire not more bright than thine eyes. With how fine an interspace do the delicate eyebrows meet upon thy forehead! How just the blend that makes thy blush, thy fairness not o'ermantled with too much red! Pinker thy fingers than Aurora's, firmer thy shoulders than Diana's; even thy mother dost thou surpass. If Bacchus, Ariadne's lover, could transform his mistress' garland into a constellation how comes it that a more beauteous maid has no crown of stars?
There is a scholarly debate about how old Maria was. This would depend on when her parents were married. Passages of "De Consulatu Stilichonis" by Claudian, reports that Stilicho first rose to fame through successfully negotiating a peace treaty with the Sassanid Empire, then was chosen by Theodosius I to marry his niece.
The Passages read: "Scarce hadst thou reached man's estate when thou wast sent to negotiate peace with Assyria;to make a treaty with so great a people was the charge entrusted to thy youth. Crossing the Tigris and the deep Euphrates thou cam'st to Babylon. The grave lords of Parthia looked at thee in amaze and the quiver-bearing mob burned with desire to behold, while the daughters of Persia gazing on their beauteous guest sighed out their hidden love. The peace is sworn at altars sweet with the fragrance of incense and the harvests of Saba. Fire is brought forth from the innermost sanctuary and the Magi sacrifice heifers according to the Chaldean ritual. The king himself dips the jewelled bowl of sacrifice and swears by the mysteries of Bel and by Mithras who guides the errant stars of heaven. Whenever they made thee sharer of their hunting, whose sword struck down the lion in close combat before that of Stilicho, whose arrow pierced the striped tiger afar before thine? When thou didst guide the easy rein the Mede gave way to thee, and the Parthian marvelled at the bow thou didst discharge in flight.
"Meanwhile a maiden of years full ripe for marriage troubled a father's heart, and the emperor doubted whom to select as her husband and as future ruler of the world; right anxiously did he search east and west for a son-in‑law worthy of being wedded to Serena. Merit alone had to decide; through camps, through cities, through nations roamed his poised and hesitating thoughts. But thou wast chosen, thus in the opinion and judgement of him who selected thee surpassing all the candidates of the whole world and becoming a son-in‑law in the imperial family where thou wast shortly to become a father-in‑law. The marriage-bed was ablaze with flashing gold and regal purple. The maiden steps forth accompanied by her parents clad in scarlet. On one side stood her sire, famed for his triumphs, on the other was the queen, fulfilling a mother's loving office and ordering the bridal veil beneath a weight of jewels. Then, so men say, the horses of the sun and the stars of heaven danced for joy, pools of honey and rivers of milk welled forth from the earth. Bosporus decked his banks with vernal flowers, and Europe, entwined with rose garlands, uplifted the torches in rivalry with Asia.
The account seems to report that (1)Stilicho negotiated the treaty of mutual friendship between Theodosius I and Shapur III (2) Theodosius I and Aelia Flaccilla acted as adoptive parents to Serena, possibly following the deaths of her natural parents. The treaty has been usually dated to 384, but dates as late as 387 have been suggested for both the treaty and the marriage following it. By any estimation, Maria would be at most fourteen-years-old at the time of her marriage.
According to the account of Zosimus, "When Maria was about to be married to Honorius, her mother, deeming her too young for the marriage-state and being unwilling to defer the marriage, although she thought that to submit so young and tender a person to the embraces of a man was offering violence to nature, she had recourse to a woman who knew how to manage such affairs, and by her means contrived that Maria should live with the emperor and share his bed, but that he should not have the power to deprive her of virginity. In the meantime Maria died a virgin, and Serena, who, as may readily be supposed, was desirous to become the grandmother of a young emperor or empress, through fear of her influence being diminished, used all her endeavours to marry her other daughter to Honorius." The account may have attempted to explain why Maria died without giving birth. However this might also be explained by the young ages of the imperial couple, the tale of Honorius being drugged by his mother-in-law Serena considered fanciful. Her sister Thermantia went on to marry Honorius.