Aphids are among the rare organisms that can change their reproductive mode across their life cycle. During spring and summer they reproduce clonally and efficiently by parthenogenesis. At the end of summer aphids perceive the shortening of day length which triggers the production of sexual individuals - males and oviparous females - that will mate and lay overwintering cold-resistant eggs. Recent large scale transcriptomic studies allowed the discovery of transcripts and functions such as nervous and hormonal signaling involved in the early steps of detection and transduction of the photoperiodic signal. Nevertheless these experiments were performed under controlled conditions when the photoperiod was the only varying parameter. To characterize the response of aphids under natural conditions, aphids were reared outdoor both in summer and autumn and material was collected to compare their transcriptomic profile using a cDNA microarray containing around 7000 transcripts. Statistical analyses revealed that close to 5% of these transcripts (367) were differentially expressed at two developmental stages of the process in response to the autumnal environmental conditions. Functional classification of regulated transcripts confirmed the putative contribution of the neuro-endocrine system in the process. Furthermore, these experiments revealed the regulation of transcripts involved in juvenile hormone synthesis and signaling pathway, confirming the key role played by these molecules in the reproductive mode switch. Aphids placed under outdoor conditions were confronted to a range of abiotic factors such as temperature fluctuations which was confirmed by the differential expression of an important proportion of heat shock protein transcripts between the two seasons. Finally, this original approach completed the understanding of genetic programs involved in aphid phenotypic plasticity.