Agassiz House is considered to be one of the oldest surviving rural villas in the Waioeka Valley, and is linked with limited ongoing Maori ownership of land in the Opotiki area following major confiscations by the colonial government in the eastern Bay of Plenty during the 1860s.

The timber villa is believed to have been constructed in circa 1898 or shortly thereafter by William (Billy) Oakes (1861-1950), an early Waioeka settler and a local carpenter of mixed Maori and Pakeha descent. As a renowned local builder, Oakes is likely to have built the moderately large house to his own specifications. Erected as the main dwelling for a 32.4 hectare (80 acre) farm, the structure is situated a few kilometres to the south of the colonial town at Opotiki. It lies on prime agricultural land in the Lower Waioeka flats, which supported traditional Maori farming practices before being used for growing maize in the late nineteenth century. Opotiki supplied produce to other centres such as Auckland both before and after the colonial takeover of the region in 1866, partly due to the quality of these soils.

Most of the Lower Waioeka was parcelled out to military and other settlers following the large-scale confiscation of land around Opotiki from Te Whakatohea. The plot on which Agassiz House sits is thought to be one of a few allocated to Maori in compensation for land taken elsewhere. It was granted to Te Aira (Ida) Horohoro in 1868 - the same year that the nearby Waioeka redoubt was strengthened against incursions from Maori groups who continued to resist confiscation. It was part of only a comparatively small proportion of land south of Opotiki granted to individual Maori. Te Aira is believed to have been given the grant in acknowledgement of her cooperation with government forces, which may have included helping the Reverend Thomas Grace to escape Pai Marire adherents in 1865. In 1897-1898, she formally passed on the land to her nephew Billy Oakes, whose boat-builder father had been one of the few Pakeha in the district prior to the 1860s. Te Aira continued to live in a whare in one corner of the property, although the house - when built - was successively leased to a Chinese resident, and another mixed Pakeha-Maori farming family, the Matchitts. Oakes derived much of his income from construction work and the ownership of properties in Opotiki, but later farmed the land from the house himself.

The house may have been occupied for a period by Louisa Eliza Agassiz (circa 1886-1981), who had been adopted by Billy Oakes' sister Ani Oakes and her husband Alfred Rowland Agassiz, according to traditional Maori, or whangai, practice. After Louisa Agassiz's death in 1981, the house was transferred to, and occupied by, Louisa's descendants. In 1994, the house was named Agassiz House after Louisa Agassiz, who was their grandmother. They have made considerable alterations in a similar style, in adapting the house to be suitable for bed and breakfast accommodation. Modifications have included the replacement of an original lean-to at the rear with an enlarged structure, the addition of a new verandah and bay window to the north, the addition of dormer windows, and a staircase to new rooms within the attic.