Ant colonies are organized into social castes that perform different functions and comprise members differing in both morphology and behavior. The caste fate of sexually reproductive 'queens' and nonreproductive 'workers' is determined during larval development, in response to environmental cues rather than by genetic differences between individuals. A new report by Bonasio et al. explores the epigenetic basis of caste specialization by comparing the DNA methylation profiles of two ant species that show caste-specific gene expression patterns. Bisulfite sequencing reveals that methylcytosines in both CpG and non-CpG contexts are highly enriched in active genes of all castes at all developmental stages. Interestingly, the intragenic methylation sites show a marked preference for exons and are largely absent from introns, which suggests that they may be positioned to influence splice-site selection. This possibility is reinforced when their distribution is examined: methylation peaks at the start of the second exon, 'patches' of methylation are observed near alternative splice sites and methylation levels are reduced at skipped exons. Both ant species show caste-specific DNA methylation patterns at genes involved in reproduction, telomere maintenance and metabolism of noncoding RNAs, and in some cases differential methylation correlates with changes in splicing patterns or gene expression levels. Remarkably, some of the caste-specific loci display monoallelic modification and expression patterns, which suggests that regulation of these loci may involve DNA imprinting mechanisms. These observations indicate potential links between DNA methylation, mRNA splicing and allele-specific expression in modulating ant gene activity to ultimately direct the developmental programs and adult behaviors that are unique to each caste. (Curr. Biol. doi:10.1016/j.cub.2012.07.042, published online 9 Aug 2012)