Its territory had formerly belonged to the Diocese of Vilna, but after the first partition of Poland it fell to Prussia.

Pope Pius VI carved out the new diocese and established its see at the Camaldolese monastery of Wigry, in a village about ten miles east of Suwałki.

By a Bull of Pius VII Warsaw was made the metropolitan see and the see of Wigry was changed to Augustów, a town founded in 1561 by King Sigismund II Augustus.

The next bishop, Ignatius Czyzewski, did not remain at Augustów, but changed his place of residence in 1823 to Sejny, a town founded in 1522 by Sigismund I the Old, and which is about twenty miles east of Suwałki.

The succeeding bishop, Nicholas John Manugiewicz, established the diocesan seminary in 1830, and for many years resided sometimes at Augustowo and then at Sejny.