<p>Very little is known about the origins and history of domestic chickens (<i>Gallus gallus domesticus</i>) in northern Europe due to a lack of existing documentary and ancient DNA evidence from this region. Therefore, we conducted ancient DNA analyses and radiocarbon dating of archaeological chicken bones from the Baltic Sea region (Finland, Estonia, and Lithuania). We sequenced a 201-bp long fragment of the mitochondrial control region as well as SNPs (single nucleotide polymorphisms) from the <i>thyroid-stimulating hormone receptor</i> (<i>TSHR</i>) gene and the <i>β-carotene dioxygenase 2</i> (<i>BCDO2</i>) gene, comparing with modern Finnish and Estonian landrace chickens, as well as with other ancient and modern chickens. All studied ancient chickens belonged to a prevalent E1 mitochondrial haplogroup, except one individual from the Åland Islands (haplogroup B). Allele frequencies differed between ancient Baltic and Finnish chickens from Åland Islands in <i>TSHR</i> and <i>BCDO2</i> genes, with Åland harbouring more individuals with grey skin. Interestingly, yellow-skinned chickens were more common in mainland Finland and Baltic countries during ancient times than in central and southern Europe. Mitochondrial haplogroup A was present in modern Finnish landrace chickens but not in ancient samples from the early Finnish Iron Age to the early modern period (3^rd–18^th century CE), indicating later introgression. Both Estonian and Finnish landrace chickens had a higher frequency of the <i>TSHR</i> wild-type allele than the modern reference samples. Based on our results, the ancient chickens from the Åland Islands differed from other ancient chickens from the Baltic Sea region, and the landrace chickens differ from other modern chickens.</p>