The long-day plant Petunia x hybrida 'Fantasy Red' was found to produce a considerable number of premature abortive flower buds when placed under short light period stress. Suppression subtractive hybridization (SSH) was performed to compare the gene expression profiles between normal and abortive petunia flower buds as induced by short light periods. Using reverse northern blotting, a total of 912 positive clones were successfully identified and sequenced, and 289 non-redundant, differentially expressed transcripts were obtained. According to the Blast2GO and KEGG pathway analyses, the significant distinct cellular component was identified as mitochondrion, and the notable different metabolic pathways were ascribed to carbohydrate metabolism and lipid metabolism. The quality of the SSH libraries was verified through quantitative real-time reverse transcription-PCR (qRT-PCR) analysis of 14 genes. In addition, six of these genes were demonstrated to be of temporal and/or spatial specificity using qRT-PCR, implying that they might be responsible for the premature flower abortion. Furthermore, Phms2 (KC465381), a sequence sharing a high degree of similarity with male sterility 2 gene was characterized, and its inconsistent expression pattern predicted a novel role for Phms2 in flower bud abortion. The data presented here provide insight into the molecular mechanisms of premature flower abortion under short light periods and, hence, may be of value for assessing candidate genes with potential for creating novel germplasms with enhanced photoperiod stress tolerance. Crown Copyright (C) 2013 Published by Elsevier B.V. All rights reserved.