It has been shown that Y-haplogroup N3a1-B211 is common in the Finnish-speaking peoples of the Ural-Volga region. The study aimed to investigate gene geography and phylogeography of the westernmost variant of this haplogroup: the N3a1-Y23475 branch. Comprehensive genotyping of 395 haplogroup N3a1-B211 carriers from 29 populations of Eastern Europe, Ural-Volga region, and Siberia revealed 78 carriers of its western branch reaching its maximum frequency in Mordovia’s populations (8% in Moksha, 9% in Erzya, 25% in Tengushevsky Erzya-Shoksha). Low N3a1-Y23475 frequencies in the Turkic-speaking and Slavic populations suggest the role of the Finnish-speaking substrate in their gene pools. According to the phylogenetic analysis data, the N3a1-Y23475 branch emerged 2.3–2.7 thousand years ago, but active accumulation of its current diversity took place mainly in the populations of Mordovia during the last millennium. We performed DNA genotyping in 74 haplogoup N3a1-Y23475 carriers using the 37 Y-STR panel. The Y-STR haplotype phylogenetic network created suggests two periods of population growth in ancestors of Mordovia’s indigenous population: about 1000 years ago in the populations of proto-Erzya and proto-Shoksha, about 500 years ago in the populations of Moksha and Shoksha. The fact of finding haplogroup N3a1-Y23475 in the Northern and Southern Altaians requires further research. Position of Northern Altaians-Kumandins in the phylogenetic network presumably reflects migration of Mordovia’s population to Altai in the 19th–20th centuries. The age estimates reported for Southern Altaians-Telengits can indicate the association with the haplogroup N3a1 ancestral homeland in South Siberia before resettlement of its ancient carriers in the Ural-Volga region about 1.7 thousand years ago.