According to Wikipedia:
Black Irish is an ambiguous term used mainly outside of Ireland. Over the course of history, and in different parts of the Irish diaspora throughout the world, it has been subject to several different although somewhat overlapping meanings, encompassing physical appearance, religious affiliation, ethnicity, subculture and poverty. Modern traditionalists, however, maintain the term to be synonymous with a dark-haired phenotype exhibited by certain individuals originally descended from Ireland. Opinions vary in regard to what is perceived as the usual physical characteristics of the so-called Black Irish: e.g., dark hair, brown eyes and medium skin tone; or dark hair, blue or green eyes and fair skin tone. Unbeknown to some who have used this term at one time or another, dark hair in people of Irish descent is extremely common, although darker skin complexions appear less frequently.
Early 21st century genetic studies have provided new insights into the origins of Irish people as well as their neighbours in the British Isles. Correspondingly, researchers in the field have suggested that migrations from Prehistoric Iberia (Spain, Portugal and also the Basque region) can be viewed as the primary source for their genetic material, having demonstrated marked similarities with modern representatives of the aforementioned time period in that of the Basque people. However, the majority of Irish males fall under the R1b sub-clade L-21, which is quite rare for Basques.
The first clear evidence of human habitation in Ireland has been carbon dated to about 7000 BC. Legends, such as those described in the Book of Invasions, refer to a number of pre-historical ethnic groups, including the Fomorians, Nemedians, Fir Bolg, Tuatha Dé Danann and Milesians. Despite the lack of empirical data linking them to the Irish, one or more of these races have been acknowledged in previous and current ancestral studies, such as Dennis O'Mullally's History of O'Mullally and Lally Clan, or The history of an Irish family through the ages intertwined with that of the Irish nation, wherein the author points to the Fir Bolg as "the aboriginal people of Ireland, smaller in stature than the Gaels, with jet-black hair and dark eyes, contrasting with unusually white skin."
The physical traits of the black Irish are sometimes thought to have been the result of an Iberian admixture originating with survivors of the Spanish Armada. Most Armada survivors were killed on the beaches, and many of the remnants eventually escaped from Ireland, but a group of Spanish soldiers ended up serving as armed retainers to the Irish chiefs Brian O'Rourke, Sorley Boy MacDonnell and Hugh O'Neill, 2nd Earl of Tyrone.
The genetic evidence is that the survivors of the Spanish Armada probably left no legacy, as the Irish have only minute amounts of Neolithic Italic Y chromosome genetic markers, such as G and J, which are present in trace levels throughout Spain. These results may be spurious as the Atlantic Modal Haplotype R1b is present in most Western European males including most Spanish and Irish males.
The Spanish Armada myth is thought to have been a corruption of a story based on the Milesians, the purported descendants of Míl Espáine (Latin Miles Hispaniae, "Soldier of Hispania", later pseudo-Latinised as "Milesius"), speculated to represent Celtic-speaking peoples from the western Iberian peninsula who began to migrate to Ireland and Britain in the fifth century B.C. Genetic research shows a strong similarity between the Y chromosome haplotypes of males from north-western Spain and northern Portugal and Irish men with Gaelic surnames. There is a significant difference between peoples of the west and the east of Ireland. Genetic marker R1b reaches frequencies as high as 98% in north-western Ireland and 95% in south-western Ireland, but drops to 73% in north-eastern Ireland and 85% in south-eastern Ireland. Additionally, R1b averages between 90% and 95% in Y chromosomes of the Basques of northern Spain (and south-western France), considerably greater than levels of the same haplogroup found amongst the remaining Spanish genepool, where it varies from region to region in a range from 42% to 75%, but mostly with percentages in the 50s and 60s.
In recently published books (Blood of the Isles by Bryan Sykes and The Origins of the British - A Genetic Detective Story by Stephen Oppenheimer), both authors propose that ancient inhabitants of Ireland can be traced back to the Iberian Peninsula, as a result of a series of migrations that took place during the Mesolithic and to a lesser extent the Neolithic Age. The Ice Age caused the depopulation of the British Isles. After glaciers retreated, the islands were populated by migrations from the Iberian Peninsula. These migrations laid the foundations for present-day populations in the British Isles, contributing three-quarters of the ancestral population, according to Oppenheimer. Later migrations of Romans, Anglo-Saxons, and Normans appear to be much less significant in terms of genetic additions than previously thought. Oppenheimer maintains there is a great lineal commonality between the Irish and British people. He also advances the controversial claim that a language closely related to Basque was long ago spoken by their shared ancestors.
A similar theory was examined in the early 1980s by Bob Quinn with his trilogy of documentary films entitled Atlantean. He argued for the existence of a west Atlantic continuum of people, and linked the region of Connemara, in Ireland's West, with Iberian and Berber types who supposedly travelled from across the sea over a period spanning several thousand years.
C. Wesley Dupertuis conducted a survey of Irish people in the 1940s under the guidance of the Department of Anthropology of Harvard University, and gathered the following data.
The hair colour of the Irish is predominantly brown The most common Hair colour is dark brown. Less than 15% have black or ashen hair; 50% have dark brown hair. Medium brown hues make up another 15%. Persons with blond and light brown hair account for close to 5%, while approximately 10% have auburn or red hair. Both golden and dark brown shades can be seen in the south-western counties of Ireland, but fairest hair in general is most common in the Central Plain. Ulster has been evidenced to have the highest frequencies of red and blonde hair, with the lowest found in Wexford and Waterford.
Studies have indicated the Irish are "almost uniquely pale skinned when unexposed, untanned parts of the body, are observed" and "40% of the entire group are freckled to some extent." Moreover, "in the proportion of pure light eyes", data shows that "Ireland competes successfully with the blondest regions of Scandinavia", as approximately 42% of the Irish population have pure blue eyes. Another 30% have been found to possess light-mixed eyes and "less than 1 half of 1% have pure brown".