Tonina experienced its golden age during the Late Classic Period although the Valley of Ocosingo was inhabited from the Late Preclassic. Steles found at the site dating as late as 909 AD suggest that Tonina resisted collapse and remained a vital society past many of its contemporaries. Because much of Tonina's ornamentation is done in stucco early depictions are non existent having been destroyed or simply eroded by the Early Postclassic. The ruined city was inhabited intermittently and its tombs reused.

Tonina is believed to have conquered Palenque and led to its eventual collapse. In the 7th century a dynast change occurred from the long standing "Lord of the Lineage of the Underworld" to the "Snake Skull-Jaguar Claw".

As customary the new ruling elite built over their predecessor's works adding their layer. During the revitalization period Palenque and surrounding villages were attacked and taken under control by the new ruling party.

Tonina reached its zenith around ten years after sacking Palenque in 730 AD. It was known as the Place of Celestial Captives having chambered many captured personages. A popular theme in Tonina sculptures is captives being decapitated or subjected to torture.

The last ruler to be immortalized by any remaining record was Jaguar Serpent in 903. This is the last period that Tonina is believed to experienced any standing as a society.

The site was explored in the twenties by the University of Tulane but it was not until the 1970s that the French researchers, Pierre Becquelin, Claud-Fracois Baudez and Eric Taladoire excavated the site.