PHYTOCHROME INTERACTING FACTOR 3-LIKE5 (PIL5) is a basic helix-loop-helix transcription factor that inhibits seed germination by regulating the expression of gibberellin (GA)- and abscisic acid (ABA)-related genes either directly or indirectly. It is not yet known, however, whether PIL5 regulates seed germination solely through GA and ABA. Here, we used Chromatin immunoprecipitation-chip (ChIP-chip) analysis to identify 748 novel PIL5 binding sites in the Arabidopsis thaliana genome. Consistent with the molecular function of PIL5 as a transcription regulator, most of the identified binding sites are located in gene promoter regions. Binding site analysis shows that PIL5 binds to its target sites mainly through the G-box motif in vivo. Microarray analysis reveals that phytochromes regulate a large number of genes mainly through PIL5 during seed germination. Comparison between the ChIP-chip and microarray data indicates that PIL5 regulates 166 genes by directly binding to their promoters. Many of the identified genes encode transcription regulators involved in hormone signaling, while some encode enzymes involved in cell wall modification. Interestingly, PIL5 directly regulates many transcription regulators of hormone signaling and indirectly regulates many genes involved in hormone metabolism. Taken together, our data indicate that PIL5 inhibits seed germination not just through GA and ABA, but also by coordinating hormone signals and modulating cell wall properties in imbibed seeds.