Human inhabitation is relatively recent and sparse in the Alutaguse region. The main prehistoric features are barrow complexes made of sand, which point to the existence a Votian community at the end of the first millennium AD and at the beginning of the second. Estonia's largest barrow complex (around 300 barrows) is situated at Jõuga. There are also many sand barrows at Kivinõmme, next to the Narva River, and in the vicinity of Iisaku and Rannapungerja.

In the 17th and 18th centuries Russian Old Believers settled in Alutaguse, mainly in the areas bordering the Narva River and around Iisaku. Because they gradually adopted Lutheranism but kept their cultural distinction, they were called ‘Poluverniks’ (‘half-breeds’). At the end of the 19th century the governor of Estonia, Prince Sergei Dahhovskoi, built the Pühitsa Orthodox Convent high on Kuremägi Hill, in order to propagate the Orthodox Church and Russian culture in North-east Estonia. Older Russian historical and cultural heritage also includes the villages on the Narva River and churches in Vasknarva, Jaamaküla, Alajõe, and Lohusuu.

Traditional occupations in Alutaguse include iron smelting from bog-ore (Rebu, Rääsa), fishing (on the Narva River and along the shores of Lake Peipsi), lumbering, rafting, and woodworking. The villages around Avinurme are particularly famed for the latter. Since there was little farmland, but a great deal of forest, woodworking craftsmanship was passed down from generation to generation. Over time, villages became specialised in one type of product. Avinurme fairs were renowned throughout Estonia.

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