The ability of rice to germinate under anoxia by extending the coleoptile is a highly unusual characteristic and a key feature underpinning the ability of rice seeds to establish in such a stressful environment. The process has been a focal point for research for many years. However, the molecular mechanisms underlying the anoxic growth of coleoptile still remain largely unknown. To unravel the key regulatory mechanisms of rice germination under the anoxic stress, we combined in silico modeling with gene expression data analysis. Our initial modeling analysis via random flux sampling revealed numerous changes in rice primary metabolism in the absence of oxygen. In particular, several reactions associated with sucrose metabolism and fermentation showed significant increase in flux levels, whereas reaction fluxes across oxidative phosphorylation, TCA cycle and pentose phosphate pathway were down-regulated. The subsequent comparative analysis of the differences in calculated fluxes with previously published gene expression data under air and anoxia identified at least 37 reactions from the rice central metabolism that are transcriptionally regulated. Additionally, cis-regulatory content analysis of these transcriptionally controlled enzymes indicate a regulatory role for transcription factors such as MYB, bZIP, ERF and ZnF in transcriptional control of genes that are up-regulated during rice germination and coleoptile elongation under anoxia.