Indian dairy production takes place in very diverse environments. The objective of this study was to identify genotype by environment interactions in the context of establishment of a reference population for genomic selection. Data from 9,265 cows in six states were analysed. The high variability in the distribution of breed types and milk yield across India, as well as the wide range of climatic zones existing in the country are highlighted. This heterogeneity must be taken into account, defining, for example, groups of districts (administrative regions within states), rather than considering India as one homogeneous country, in order to better predict the genomic merit of individuals in their local environment.