With the election of Evo Morales and his party Movement to Socialism (MAS) in 2005, Bolivia has become the only country in Latin America to have an indigenous party in power. However, it is misleading to take the MAS government as representing all of Bolivia’s ethnic diversity. Its indigenous population can be classified into peoples from the Andean highlands and from the Amazonian lowlands. Research has treated the indigenous population as uniform or focused on the Andean peoples and on parties rather than voters. This paper aims to differentiate this picture by showing that variances between highland and lowland indigenous peoples started with the appearance of Homeland’s Consciousness (CONDEPA) and have increased since MAS came to power. While the highland indigenous peoples have preferred left political parties, parties with pro-indigenous agendas or which used indigenous symbolism, the lowland peoples have tended to support centre-right parties. The paper attempts to explain these differences in the voting behaviour of Bolivia’s indigenous peoples. Ethnic voting is analysed in the time span from 1985 until 2014 within a mixed-methods design.