structural:summarization
Genetic origins

The distinctiveness noted by studies of 'classical' genetic markers (such as blood groups) and the apparently " pre-Indo-European " nature of the Basque language has resulted in a popular and long-held misleading view that Basques are "living fossils" of the earliest modern humans who colonised Europe. Partly for these reasons, anthropological and genetic studies from the beginning and the end of the 20th century theorized that the Basques are the descendants of the original Cro-Magnons.

But although they are genetically distinctive in some ways due to isolation, the Basques are still very typically European in their Y-DNA and mtDNA sequences, and in some other genetic loci. These same sequences are widespread throughout the Western half of Europe, especially along the Western fringe of the continent.

Autosomal genetic studies have confirmed that Basques share close genetic ties to other Europeans, especially with Spaniards, who have a common genetic identity of over 70 % with Basques, a homogeneity amongst both their Spanish and French populations, according to high-density SNP genotyping study done in May 2010, and a genomic distinctiveness, relative to other European populations.

Studies of the Y-DNA haplogroups found that on their direct male lineages, the vast majority of modern Basques have a common ancestry with other Western Europeans, namely a marked predominance of Haplogroup R1b-DF27 (70 % according to some). This had initially been theorised to be a Palaeolithic marker. But this theory encountered inconsistencies even prior to the most recent chronological re-evaluations. More recent studies suggest that R1b spread up to Western Europe from southwestern Eurasia in the Neolithic period or later, between 8,000 and 4,000 years ago. The age of the subclade which Basques carry, R1b-DF27, "is estimated at ~4,200 years ago, at the transition between the Neolithic and the Bronze Age, when the Y chromosome landscape of Western Europe was thoroughly remodeled. In spite of its high frequency in Basques, Y-STR internal diversity of R1b-DF27 is lower there, and results in more recent age estimates", implying it was brought to the region from elsewhere. Next to the main lineage R1b, high frequencies of E-V65, associated with the Maghreb, Italy and Spain, were found among Basque autochthonous inhabitants of Álava province (17.3 %), Biscay province (10.9 %), and Gipuzkoa province (3.3 %).

Several ancient DNA samples have been recovered and amplified from the Iberian and Basque region. The collection of mtDNA and Y-DNA haplogroups sampled there differed significantly compared to their modern frequencies. The authors concluded that there is "discontinuity" between ancient locals and modern Basques. While Basques harbour some very archaic mtDNA lineages, they are not of "undiluted Palaeolithic ancestry" but of significantly early Neolithic origin with a connection to the isolate Sardinian people. It appears that some 4,500 years ago almost all Y-DNA heritage from Iberian admixture of Mesolithic hunter-gatherers and Neolithic farmers was replaced by the R1b lineage of herders from the steppe, and the Basque genetic distinctiveness is a result of centuries of low population size, genetic drift, and endogamy.

In 2015, a new scientific study of Basque DNA was published which seems to indicate that Basques are descendants of Neolithic farmers who mixed with local Mesolithic hunters before becoming genetically isolated from the rest of Europe for millennia. Mattias Jakobsson from Uppsala University in Sweden analysed genetic material from eight Stone Age human skeletons found in El Portalón Cavern in Atapuerca, northern Spain. These individuals lived between 3,500 and 5,500 years ago, after the transition to farming in southwest Europe. The results show that these early Iberian farmers are the closest ancestors to present-day Basques. The findings were published in Proceedings of the National Academy of Sciences of the United States of America. According to the study, the "results show that the Basques trace their ancestry to early farming groups from Iberia, which contradicts previous views of them being a remnant population that trace their ancestry to Mesolithic hunter-gatherer groups." Still these early Neolithic farmer ancestors of the Basques did mix with local southwestern hunter-gatherers, and "the proportion of hunter gatherer-related admixture into early farmers also increased over the course of two millennia." This admixed group was also found to be ancestral to other modern-day Iberian peoples, but while the Basques remained relatively isolated for millennia after this time, later migrations into Iberia led to distinct and additional admixture in all other Iberian groups.

In 2019, a study was published in Science in which a more modern time-transect of Iberian ancient populations including the Basque were analyzed. From their abstract, it says: "and we reveal that present-day Basques are best described as a typical Iron Age population without the admixture events that later affected the rest of Iberia." This indicates Basques were isolated from admixture with outside groups since at least 1000 BC, or 3000 years before the present. In Iberia, these later admixture (interbreeding) events were with central European (Celtic), eastern Mediterranean (Phoenician, Greek and Roman), northern African (Carthaginian and Mauritanian) and northern European (Gothic and Frankish) populations, and genomic ancestry from them are found in varying degrees in all or most present-day Iberian populations, except – albeit to a limited extent even there – for the Basque.