Understanding whether natural populations will be able to adapt to rapid climatic change is a major research priority. We are using an evolutionarily young and ecologically important clade of eight rainbowfish species to understand adaptive resilience and to test predictions from the ‘climatic variability hypothesis’ for the major climatic regions of Australia. Here we present results from mechanistic transcriptomic studies in the lab and in the wild and from range-wide landscape genomic surveys for (i) a desert, (ii) a subtropical, and (iii) a temperate rainbowfish species (i.e. three major ecotypes). Our datasets include a whole de novo genome and three de novo transcriptomes (all annotated), transcriptomic (RNAseq) profiles for experimental and wild populations, phenotyping of adaptive traits, and genome-wide ddRAD SNPs for 51 populations / 1,020 individuals. Although the three species shared 80.9% of their 37,160 unigenes, climate change experiments revealed major differences in gene expression associated with future climates (only 2.1% of genes were shared between species). Transcriptomic profiles of wild populations along a latitudinal region indicate that candidate genes for high expression divergence (i.e. more variance among- compared to within-populations) correlate better with the environmental gradient than those showing high expression plasticity. Landscape genomics provided evidence for adaptive divergence associated with hydrological unpredictability (desert) and with major hydroclimatic gradients (temperate and subtropical), as well as for balancing selection in more variable environments (subtropical species). Rainbowfishes represent an ideal model system for clarifying climatic and geographic correlates of adaptation and for disentangling plastic from evolutionary responses to climate change.