Heterosis is a fundamental biological phenomenon defined by the superior performance of hybrids over its parents in many economically important traits. Even though heterosis has been extensively used in agriculture, both in plants and animals, the underlying molecular basis remains elusive. This lack of knowledge hampers the rational design of hybrids in order to obtain, in a faster and more efficient way, benefits resulting from heterotic effects. Evidence obtained from several species allows hypothesizing that alterations in the epigenetic state, mediated by changes in the DNA methylation pattern, play a role in determining hybrid vigor. Nevertheless, how parental alleles interact in their progeny to influence the epigenome is poorly understood. We analyzed DNA methylomes, siRNAomes and transcriptomes of three tomato hybrids, and their corresponding divergent parents. Interestingly, the parental methylation, siRNAs and transcriptome patterns did not correlate with the genetic distance between the genotypes and several genes involved in key metabolic categories showed to be epigenetically regulated. Evenmore, hybrids displayed non-additive DNA methylation levels throughout the genome. These results add to the growing evidences that point epigenetic mechanisms as key determinants of hybrid performance and make them able to future applications in breeding programs.