Meanwhile, Nguyen Kim, a former official in the Le court, revolted against the Mac and helped king Le Trang Tong restore the Le court in the Thanh Hoa area. Thus a civil war began between the Northern Court (Mac) and the Southern Court (Restored Le). Nguyen Kim's side controlled the southern part of Đại Việt (from Thanhhoa to the south), leaving the north (including Đông Kinh-Hanoi) under Mạc control. When Nguyen Kim was assassinated in 1545, military power fell into the hands of his son-in-law, Trinh Kiem. In 1558, Nguyen Kim's son, Nguyen Hoang, suspecting that Trinh Kiem might kill him as his brother to secure power, asked to be governor of the far south provinces (around present-day Quang Binh to Binh Dinh). He governed the south effectively while Trinh Kiem, and then his son Trinh Tung, carried on the war against the Mac. Nguyen Hoang sent money and soldiers north to help the war but gradually he became more and more independent.

The civil war between the Le/Trinh and Mạc dynasties ended in 1592, when the army of Trinh Tung conquered Hanoi and executed king Mac Mau Hop. Survivors of the Mac royal family fled to the northern mountains in the province of Cao Bang and continued to rule there until 1667 when Trinh Tac conquered this last Mac territory. The Le kings, ever since Nguyen Kim's restoration, only acted as figureheads. After the fall of the Mac Dynasty, all real power in the north belonged to the Trinh Lords.

In the year 1600, Nguyen Hoang also declared himself Lord (officially "Vương", popularly "Chúa") and refused to send more money or soldiers to help the Trinh. He also moved his capital to a new place, Phu Xuan (modern-day Hue). Nguyen Hoang died in 1613 after having ruled the south for 55 years. He was succeeded by his 6th son, Nguyen Phuc Nguyen, who likewise refused to acknowledge the power of the Trinh, yet still pledged allegiance to the Le king.

Trịnh Tráng succeeded Trinh Tung, his father, upon his death in 1623. Tráng ordered Nguyen Phuc Nguyen to submit to his authority. The order was refused twice. In 1627, Trinh Trang sent 150000 troops southward in an unsuccessful military campaign.

Map of Vietnam showing (roughly) the areas controlled by the Trịnh, Nguyen, Mac, and Champa about the year 1640 One of the earliest Western maps of Vietnam, published in 1651 by Alexandre de Rhodes (north is oriented to the right)The Trinh-Nguyen War lasted from 1627 until 1672. The Trinh army staged at least seven offensives, all of which failed to capture Phú Xuan. For a time, starting in 1651, the Nguyen themselves went on the offensive and attacked parts of Trịnh territory. However, the Trịnh, under a new leader, Trinh Tac, forced the Nguyễn back by 1655. After one last offensive in 1672, Trinh Tac agreed to a truce with the Nguyen Lord Nguyen Phuc Tan. The country was effectively divided in two.

The Trịnh and the Nguyen maintained a relative peace for the next 100 years, during which both sides made significant accomplishments. The Trinh created centralized government offices in charge of state budget and producing currency, unified the weight units into a decimal system, established printing shops to reduce the need to import printed materials from China, opened a military academy, and compiled history books.

Meanwhile, the Nguyen Lords continued the southward expansion by the conquest of the remaining Cham land. Viet settlers also arrived in the sparsely populated area known as "Water Chenla", which was the lower Mekong Delta portion of Chenla (present-day Cambodia). Between the mid-17th century to mid-18th century, as Chenla was weakened by internal strife and Siamese invasions, the Nguyễn Lords used various means, political marriage, diplomatic pressure, political and military favors,... to gain the area around present day Saigon and the Mekong Delta. The Nguyễn army at times also clashed with the Siamese army to establish influence over Chenla.

In 1771, the Tay Son revolution broke out in Quy nhơn, which was under the control of the Nguyen Lord. The leaders of this revolution were three brothers named Nguyen Nhac, Nguyen Lu, and Nguyen Hue (not related to the Nguyen lords). By 1776, the Tay Son had occupied all of the Nguyen Lord's land and killed (almost) the entire royal family. The surviving prince Nguyen Phuc Anh (often called Nguyen Anh) fled to Siam, and obtained military support from the Siamese king. Nguyen Anh came back with 50000 Siamese troops to regain power, but was defeated at the Battle of Rach Gam–Xoai Mut and almost killed. Nguyen Anh fled Vietnam, but he did not give up.

The Tay Son army commanded by Nguyen Hue marched north in 1786 to fight the Trinh Lord, Trinh Khai. The Trinh army failed to defend and Trinh Khai committed suicide. The Tay Son army captured the capital in less than two months. The last Le emperor, Le Chieu Thong, fled to China and petitioned the Chinese Qing Emperor for help. The Qing emperor Qianlong supplied Le Chieu Thong with a massive army (about 200000 men) to regain his throne from the usurper. Nguyễn Huệ proclaimed himself Emperor Quang Trung and defeated Qing troops (with 100000 men) in a surprise 7 day campaign during the lunar new year (Tết). During his reign, Quang Trung envisioned many reforms but died by unknown reason on the way march south in 1792, at the age of 40.

During the reign of Emperor Quang Trung, Dai Viet was actually divided into 3 political entities. The Tay Son leader, Nguyen Nhac, ruled the Central of the country from his capital Qui Nhơn. Emperor Quang Trung ruled the North from the capital Phu xuan Hue. In the South, Nguyen Anh, assisted by many talented recruits from the South, captured Gia Dinh (present day Saigon) in 1788 and established a strong base for his force.

After Quang Trung's death, the Tay Son Dynasty became unstable as the remaining brothers fought against each other and against the people who were loyal to Nguyen Hue's infant son. Nguyen Anh, sailed north in 1799, capturing Tay Son's stronghold Qui Nhơn. In 1801, his force took Phú Xuân, the Tây Sơn capital. Nguyen Anh finally won the war in 1802, when he sieged Thang Long (Hanoi) and executed Nguyen Hue's son, Nguyen Quang Toan, along with many Tây Sơn generals and officials. Nguyễn Ánh ascended the throne and called himself Emperor Gia Long. Gia is for Gia Dinh, the old name of Saigon; Long is for Thang Long, the old name of Hanoi. Hence Gia Long implied the unification of the country. The Nguyễn dynasty lasted until Bảo Đại's abdication in 1945. As China for centuries had referred to Dai Viet as Annam, Gia Long asked the Chinese Qing emperor to rename the country, from Annam to Nam Viet. To prevent any confusion of Gia Long's kingdom with Trieu Da's ancient kingdom, the Chinese emperor reversed the order of the two words to Việt Nam. The name Vietnam is thus known to be used since Emperor Gia Long's reign (but recently historians have found that this name had existed in older books in which Vietnamese called their country Vietnam).

The Period of Division with many tragedies and dramatic historical developments inspired many poets and gave rise to some Vietnamese masterpieces in verse such as the epic poem The Tale of Kieu (Truyện Kiều) by Nguyễn Du, Song of a Soldier's Wife (Chinh Phụ Ngâm) by Dang Tran Con (Chinese script version) and Đoan Thi Điem (Nôm version), and a collection of satirical, erotically charged poems by the female poet Ho Xuan Huong.