In the thesis presented here a variety of methods and approaches are used to describe methylation profiles, in different tissues and stages, and its potential role in plasticity and thermal response in the cockroach Diploptera punctata and two water flea species: Daphnia magna and Daphnia lumholtzi. In the viviparous cockroach Diploptera punctata I studied how metabolic rate and life-history traits respond to temperature. I found that the metabolic rate is adaptive and highly plastic in response to temperature. Several his- tory traits were also affected by temperature, for example, developmental time, number of surviving offspring and time to reach sexual maturity. In Diploptera punctata I further describe, for the first time, tissue-specific high methylation levels, and show hydroxymethylation presence exclusively in the brain. I also demostrate that DNA methylation global levels and patterns are responsive to the environment, as they respond to diet and temperature. However, methylation patterns are also shown to be linked to the genotype. In Daphnia magna, I investigated the methylation profiles in the oocyte and early embryogenic stages where I found evidence of differentially methylated sites among stages, but more importantly, we found evidence of almost full methylation reprogramming in this species. Finally, high morphological plasticity in response to predator presence is reported in the LA2 Daphnia lumholtzi clone, among with the first draft genome and transcriptome of this species.