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Calapan City was formerly a small village before the establishment of the first Religious District in Baco. The district convent was transferred to Calapan City in 1733 and began its jurisdiction over the Northern Mindoro Ecclesiastical Area.

In the early 18th century, the town occupied only a strip of land stretching from Ibaba to Ilaya in a cross-formed facing the present church and cut-off by a river. In the course of the century, succeeding barrios were founded.

In 1873, the capital of the province was oved from Puerto Galera to Calapan City. When Mindoro became a part of Marinduque on June 13, 1902, under Act. No. 423, the capital of Mindoro was transferred to Puerto Galera under the Law. It was re-transferred to Calapan City in 1903 for geographical and transportation purposes. 

When Mindoro was detached from Marinduque on November 10, 1902, Baco, Puerto Galera and San Teodoro were annexed to Calapan City in 1905 under Act. 1280, adding a total area of 843 sq. km. of land. In 1902, under Act 2824, the three (3) municipalities gained their independence. 

In 1919, the boundary dispute between Calapan City and Naujan was adjudicated by President Agustin Quijano of Calapan and Agustin Garong of Naujan over a portion of territory of what is now known as the present boundary. The portion of agricultural area was awarded to Naujan, thus, making the area of Calapan City much smaller as compared to that of Naujan which is now considered as the biggest municipality of the province. 

At present Calapan City has an area of only 250.06 sq.km. (according to LMB). It has also jurisdiction over the three (3) Baco Islets on the Calapan Bay and the two (2) Silonay Islets.

The City of Calapan has been transformed as a component city on March 21, 1998. Its conversion was based on Republic Act 8475, enacted by Congress and signed into law by the President Fidel V. Ramos on February 2, 1998. In a plebiscite held on March 21, 1998, majority of Calapeños ratified the conversion of Calapan into a city. It is the first and only city in the province of Oriental Mindoro.