The name Dagana is derived from two sources – Darkala from the province’s guardian deity Jomo Darkala, and Darkarnang (The Realm of White Prayer Flags) from Dudjom Jigdrol Yeshey Dorji, a great Buddhist master. In the past, Darkala was also known as Ling Sum-the three vast lands which are the villages of Lha Ling, Pel Ling and Dar Ling.
The Daga Dzong was traditionally the stronghold of the powerful Daga Penlop who held the rank of cabinet minister under the Desi (temporal ruler) system of government introduced by Zhabdrung Ngawang Namgyel in 1651. Today, the Dzong houses the clergy and the headquarters of the district administration of Dagana.

By mid-17th century, Zhabdrung Ngawang Namgyel had unified most of the Western part of present-day Bhutan after a series of successful military campaigns. The Zhabdrung then turned his attention towards the south, east and central Bhutan.
In 1648 the deputized Dronyer Druk Namgyel to Darkala to bring the area under the Drukpa rule and to build a Dzong to defend the country from the invading armies of the south and the Duar areas in present-day Indian states of Assam and West Bengal. The purpose of the military expedition was achieved and Druk Namgyel began laying the foundations for the Dzong.
A strategic site, a ridge overlooking an expansive valley, was chosen and the construction began with labour contributed by the people of Darkala. Two years later in 1651 the Dzong was completed and was formally named by the Zhabdrung as Darkar Trashiyangtse Dzong, the fortress of the realm of white auspicious flags of fortune.
The paramount feature of Darkala Trashiyangtse Dzong is its utse, its central tower, which dominates the other structures of the Dzong. The exceptional height of the utse is attributed to defensive purposes as no separate Ta Dzong, watch tower, was built. The Bhutanese forces could also use the advantage of the all utse for preemptive strikes against invading armies.