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Santo Tomas was established as a separate municipality by virtue of Philippine Commission No. 347. An Act declaring the barrios of Igang, Kul-la-labo, Bulinaw, Kanyogan, Wawang, Banko,Tal-lak, Agub, Log and Taranka. Now forming the part of the municipality of Kabagan Nuevo, Province of Isabela to a new municipality under the name of Santo Tomas.
By virtue of the President of the United States, as enacted by the United States of Philippine Commission in section 011, all barrios above-mentioned are forming part of the municipality of Kabagan Nuevo, Province of Isabela, are hereby separated from said municipality and shall be organized under the Municipal Code into a new municipality under the name of Santo Tomas.
The Provincial Supervisor of Isabela surveyed the new municipality in order to establish the definite and precise boundary lines that separate it from the adjacent municipalities. The boundary lines of the municipality were established, after which, Provincial Board approved it, thus, Municipal Election shall be held in such municipality in accordance with the provisions of Articles ninety-one (91), ninety- two (92), ninety three (93), and ninety four (94) of the Municipal code.
However, there was no record available in following up the political development of this Town until the year 1917. In 1918, Santo Tomas was reverted as part of Cabagan.
Finally, through the Executive No. 199 signed by President Elpidio Quirino, Santo Tomas was separated from its mother municipality on July 01, 1949
This town derived its name from two persons who were pioneers in the area. They were Tomas Gatan and Tomas Bautista.