In Indonesia, cross-breeding local cattle with European beef breeds is widely promoted to stimulate beef production. This cross-breeding is threatening local breeds that have often different functions, including cultural roles. This study analysed the cultural values of Madura cattle and the effects of cross-breeding on local traditions in Madura Island. Bull racing (karapan) and cow conformation contests (sonok) are traditional cultural events on Madura. Since 2001, cross-breeding with Limousin is allowed. The local government also promotes a conformation contest for cross-bred (madrasin) cattle. Quantitative and qualitative information were collected through participatory approaches involving farmers (n = 97), government officials, community groups, key informants and through direct observation of sonok, karapan and madrasin events. Phenotypic characteristics were collected from 184 cows. The Madura cattle population and production systems are not homogeneous. Four cattle types could be distinguished: karapan, sonok, madrasin and conventional Madura cattle. These cattle were found in three discrete areas, differing in land sizes, cropping and cattle keeping in terms of management practices and importance of specific cultural practices. Sonok and madrasin cows were significantly bigger and had higher body condition scores than karapan cows and the conventional Madura cows in the madrasin area. Madura cattle participating in cultural events were valued at prices that were 2–3.5 times higher than Madura cattle not participating in cultural events. Cross-breeding will not directly influence the cultural events or the management practices of Madura cattle in the karapan and sonok areas; however, outside the karapan and sonok areas, crossbreds are rapidly replacing conventional Madura cattle. The present top-down approach towards conservation and breeding strategies has to be turned into bottom-up approaches that consider the needs of the sonok and karapan Madura cattle sub-populations. Monitoring and characterization studies have to collect information at different aggregation levels and have to be aware of the sub-populations. The Madura example shows that the cultural values of livestock can be a main driver for maintaining relatively small populations of local breeds.