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Arms

Stephen's rule consolidated the usage of the coat of arms of Moldavia, featuring the aurochs head (first attested in 1387), sometimes as a helmet atop his personal arms. He revived the elaborate design introduced under Alexander the Good, which also featured a rose, crescent, sun and star (often, but not always, five-pointed); its tinctures remain unknown. This arrangement was not familiar to heraldists in Western Europe. By the 1530s, they represented Moldavia with attributed arms featuring Maures; these arms, though originally used for Wallachia, possibly echoed Stephen's victories over the Ottomans.

The personal arms and heraldic flags used by Stephen have been the topic of additional scrutiny and debate. Stephen is known to have used a party per cross shield with one striped quarter, but the colors are uncertain: one prevailing interpretation is that the dominant tinctures were or and vert, although they may also have been gules and argent. These may derive from the colors used by the House of Basarab (which were possibly used by Stephen's in-law Radu the Handsome), from the coat of arms of Hungary, or from a purely Moldavian tradition. The division and the striped pattern are possibly Hungarian; they survived in some of Stephen's seals even during his dispute with the Hungarian crown. He also continued to use the fleur-de-lis, an Angevin symbol, but altered it into a "double-headed lily", then renounced it altogether. Similarly, he used the Cross of Lorraine, pattée, possibly in reference to the Pahonia. Following his 1489 dispute with Poland, that charge was altered into a double cross fleury.

Stephen's heraldic symbols progressively merged with those attributed to the House of Mușat, and were intensively used by all princes who claimed full or partial descent from Alexander the Good—including Peter the Lame, a Wallachian pretender to Moldavia's throne. The Putna tombstones of Stephen's two sons who died during his lifetime, Bogdan and Peter, already display the aurochs within the "Mușat coat-of-arms".

A Moldavian banner also survives in hand-colored versions illustrating Johannes de Thurocz 's Chronica Hungarorum, with varying tinctures. These were first identified as Stephen's flags by Constantin Karadja, and described by later authors as a version of the or-an-vert scheme in the coat of arms. Other clues suggest that the field was a solid one of or, charged with an aurochs of or, but also that the preferred "single Moldavian" color was gules. Gules is also the color of Stephen's alleged war flag, defaced with an icon of Saint George and the Dragon and donated by the prince himself to Zograf monastery. However, scholar Petre Ș. Năsturel cautions that this may not be a heraldic object of any kind, but rather a votive offering. The "war flag", he notes, is too small to carry in battle, and does not match with images in either Thurocz or Marcin Bielski, nor with the description in Alexander Guagnini.