With the demise of Zhabdrung in 1651, once again, the country fell into turmoil for a period of about 200 years. The death was initially kept secret for fifty-four years – having come to light only in 1705 – in hopes of avoiding agitation but the efforts were in vain. At first, the Desis’ resumed control of the state as the supposed rulers, but these Desis too gradually started losing their dominance over to Poenlops (Provincial governor). Inevitably, the country was divided into semi-independent regions each headed by its own Penlops. Penlop, perhaps, can be likened to the Daimyo of Japan. Like Daimyos, these Penlops are masters of their own domain and are only a step below Desi, similar to the Daimyo-Shogun dynamic. Yet, there were some Daimyos who were equally or sometimes even more powerful than Shogun. In this manner, the same could be said with Penlops and Desis. Some Penlops, especially, that of Trongsa and Paro, exercised more authority compared to Desis.

It was around that time when the activities around the Duar also started increasing and also when Bhutan first came into contact with the British East India Company. Bhutanese forces had successfully taken control of Cooch Behar and so the Raja of the state sought aid from BEIC and they successfully drove out the Bhutanese. Later the British attacked themselves of their own accord. A peace treaty was signed between the two but this didn’t prove effective as the raids on the border resumed (for some hundred years) eventually leading to the Duar War resulting in Bhutan's loss. After the whole event, the Treaty of Sinchula was signed marking the end of all hostilities between the two Nations.

In the 1870s, civil wars broke out, in large, owing to the clash between Paro and Trongsa Valley. After a series of bloodshed, and power struggles Ugyen Wangchuck, then the Trongsa Penlop emerged victorious and put an end to all of the internal strifes.

In 1907, representatives from monk bodies, heads of important families, and government officials came together and elected Ugyen Wangchuk, the Druk Gyalpo (dragon king) of Bhutan. This was the beginning of the Wangchuck dynasty.

In 1910, the Treaty of Punakha was signed between Ugyen Wangchuck and the British which ensured that the latter would not interfere in the internal affairs of Bhutan provided the king accepted their advice concerning external matters.

Ugyen Wangchuk’s son Jigme Wangchuck acceded to the throne at the age of 22. During his reign, India was freed from the British dominion, and in recognition of each other’s independence, a treaty between the two nations was signed – the Treaty of Peace and Friendship. Similar to the previous one, India was not to interfere in Bhutan’s affairs but would guide their foreign policy. Modern development foundations were to be laid.

With the succession of Jigme Dorji Wangchuk to the throne, the country slowly started opening its doors to the outside world and would usher in a modern era. Development of new modern roads, health institutions, and modern education was put into effect.

Government institutions were also reformed. The National Assembly, The Royal Bhutanese Army, and The Royal Court of Justice were established. Bhutan joined the Universal Postal Union and later also became a member of the United Nations in 1971.

In the 1870s, civil wars broke out, in large, owing to the clash between Paro and Trongsa Valley. After a series of bloodshed, and power struggles Ugyen Wangchuck, then the Trongsa Penlop emerged victorious and put an end to all of the internal strifes.

In 1907, representatives from monk bodies, heads of important families, and government officials came together and elected Ugyen Wangchuk, the Druk Gyalpo (dragon king) of Bhutan. This was the beginning of the Wangchuck dynasty.

In 1910, the Treaty of Punakha was signed between Ugyen Wangchuck and the British which ensured that the latter would not interfere in the internal affairs of Bhutan provided the king accepted their advice concerning external matters.