The oldest mention of the Núñez family in Santiago is in 1606 where various members of this family were mentioned in a census conducted by Governor Antonio de Osorio.

Vecinos de la ciudad de Santiago de los Caballeros

• Pedro Núñez, owner of an estancia de casave, mais, y tabaco.

• Jorge Núñez

• Juana Núñez

• María Núñez

Soon after this census, Isidro Núñez, a public notary in the city of Santiago de los Caballeros in 1612, appears in the records. It is unknown how he or any of the aforementioned Núñez connect with the documented ancestors of the Núñez family, but the name Isidro was carried on.

Capitán Fernándo Núñez de Caraballo married Ana María del Monte y Muñoz de Mena, daughter of Domingo del Monte Pichardo and Luisa Mena de San Miguel and had Fernando Félix Caraballo y Pichardo. Fernándo died January 1656 in Santiago.

In 1717, a Simón Núñez was mentioned connected to the Alcalde of Santiago, Don Antonio Pichardo.

In 1721 during a rebellion in Santiago, there were three Núñez mentioned in the subsequent court case: Bernardo Núñez (born 1690 in Santo Domingo, vecino de Santiago, literate, murderer of Juan Beltran), Leonardo Núñez (vecino de Santiago), and Pedro Núñez, (vecino de Santiago, Pardo libre).

Originally it was believed that the first generation of the Núñez began with an individual known as Isidoro Núñez who had Isidro Núñez (husband of María Reynoso) and José Núñez ( husband of Dionisia/Catalina de los Reyes). Y-DNA testing has disproven this genealogy as the Y-DNA of descendants of Isidro and José Núñez wound up being from different lineages. Geographically, the families are still close so it is likely there is a surname connection with one of them through the female line, but with the limited records from this time it is difficult to say. My personal opinion is that the descendants of Isidro Núñez are from the legitimate surname origin based on having more Y-DNA matches with unconnected genealogy.

In 1776, a Joseph Núñez of Estancia Nueva possessed two illegal slaves, Francisco and Margarita, and had to pay 44 pesos to to government for evading taxes. It is possible this is the same José Núñez who founded the Núñez de los Reyes family. Other Núñez remained in and close to the city while also branching out to other parts of Cibao. In 1784, los Terreno en el paraje Las Matas de Santa Cruz were owned by Juan Núñez who sold it to Francisco Espaillat for 350 pesos for raising livestock.

On February 15, 1804, Francisca Núñez the widow of granadero del regimiento de Cantabria Manuel Boriñaga, remarried, now living in Cuba requested the pension of her deceased husband as an emigrant of Santo Domingo. In the early 1800s, various families from Santiago made their way to Santo Domingo during the España Boba period. Of these families, branches of the Núñez were baptizing their children in the capital.

• 1807 - María de la Paz de los Santos y Núñez, daughter of Félix de los Santos and Theresa Núñez, naturales de Santiago

• 1807 - Manuel Núñez, son of Gregoria Núñez, natural de Santiago

• 1808 - Ramón Cayetano Núñez, son of María Núñez, natural de Santiago

• 1812 - Pedro Tomás Núñez, son of Gregoria Núñez, vecina de la Ciudad de Santiago

In 1805, multiple whites were killed in the city of Santiago under the order of future President and King of Haiti, Henri Christophe. On February 26, a group of men and women were killed including José Núñez and Juan Núñez. They were hanged at the entrance of the town hall in the city. This account was recorded by Gaspar de Arredondo y Pichardo after fleeing to Cuba. It is possible that these two were the father and son José Núñez and Juan Núñez de los Reyes though there is no way to confirm this.

In 1803, there was a division of the French military on the island specifically for members of the Spanish side of the island mostly composed of men from the Cibao, specifically Santiago and La Vega. In a military hospital in Fort-Dauphin (today Fort-Liberté) various members of the Spanish National Guard (Garde Nationale Espagnole) were treated. Two of these men were Simon Nougnez and Quiettan Nougnez, natives of Santiago, Cibao. I suspect they were actually named Simón Núñez and Quintín Núñez.

In 1826, Manuel Núñez Tineo, the son of Felipe Núñez de los Reyes and Ana Tineo Jimenez, married his cousin Maria Bonifacia Fernandez Tavares. In his testimony he inherited 50 pesos of land in la Angostura from his father.

In the mid 1800s, José María Núñez Valerio went to Baitoa and settled a branch of the family that remains there today. 

A Bartolomé Núñez was one of the first inhabitants of La Vega. (Pasajeros a la Española, 1492-1530, pg. 519)

The haplogroup for the Núñez descended from Isidro Núñez is R-ZZ12. This haplogroup is estimated to have been formed about 2520 BCE.  There is a Big Y test in progress for this lineage, so there will be major refinement of this section when that test is completed. Preliminarily, the tester matches descendants of the haplogroup R-Y21422.

There are three Núñez families that are connected to this lineage, Isidro Núñez, Santiago Núñez of San José de las Matas, and Santiago Núñez of Guayabal, Santiago.