As we know, any morphological changes in any species means changes in their gene or nucleotide sequences. If there is change in the colour of wings of same butterfly species in different seasons then there may be possibility of change in their gene also.
In diverse genera (eg., plankton and birds), diet can influence color. Is this possible in your subjects?
Phenotype reflects the genetic information, true, but this is through development. Part of the inherited information dictates how expression should be under different circumstances, this is called plasticity. Some organisms mat vary widely depending on the conditions during embryonic and postembryonic development, others not so much. In polyphenic organisms the seasonal morphs are believed to result from relativelly well fixed ('canalized') pathways (seasonal morphs), other times there are gradients in the expression of some features... all (in theory) done by the same genes (this is my guess!)
As Enrique pointed out, this phenomenon is called phenotypic plasticity, which is essentially the potential to develop different phenotypes from a single genotype. The genes themselves do not change. For a readable and elaborate explanation, I suggest you start reading this:
http://www.eeb.cornell.edu/agrawal/pdfs/whitman-and-agrawal-2009-Ch_1-Phenotypic-Plasticity-of-Insects.pdf
For several butterfly species it is known that offspring from the same mated pair will develop into one or the other wing colour phenotype depending on the environment in which the larvae are raised, in particular the photoperiod (which tells the individual what time of the year it is). Thus the different phenotypes can arise from the same genes and from the same DNA sequences, depending on which genes are activated. However, there can be slight differences between genotypes affecting how likely it is for one or the other phenotype to develop in conditions where the environment gives an unreliable signal (for instance photoperiods close to the "critical" daylength, where 50% go one way and 50% the other).
Article Induction of diapause and seasonal morphs in butterflies and...
I'm not expert in this area by any means and I'm largely unaware of the research in this area, but I think it is certainly worth looking at, the phenotypes generated can differ in far more than wing color (I was a keen entomologist as a child) and the Map butterfly for example shows a very large lifespan differential between winter and summer forms which likely represents the change in expression of a wide variety of genes involved in self maintenance. This regulation could be epigenetic in nature and thus involve changes to DNA in terms of cytosine methylation etc. In addition there are a number of parasitic protozoa which appears to perform major surgery upon their genomes during their life cycles so it may not be completely out of the question for similar events to occur in other systems.
I recalled this by H. Van Dyck & J. Windig (2009): 'Adaptation and plasticity in butterflies: the interplay of genes and environement', pp. 159-170 in Settele et al (eds), Ecology of butterflies in Europe. The text might be not available online but perhaps the authors are in RG...
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