Multiple transcription factors often interact at their genomic binding sites and these interactions enhance transcription specificity and pleiotropic functions in the regulation of diverse cellular processes. Insulin/insulin-like growth factor signaling (IIS) plays important roles in animal growth, metabolism, stress resistance and aging. It functions through the downstream forkhead transcription factor FOXO and interlays with many other key signaling pathways. The interaction between FOXO and its co-factors enhances the transcriptional specificity of insulin/FOXO signaling. We recently identified an intriguing interaction between dFOXO and zinc finger transcription factor Kruppel homolog 1 (Kr-h1). In the study, we further characterized this interaction at the genomic level to identify their direct target genes using Next-Gen sequencing approaches (ChIP-Seq and RNA-Seq). Pathway analysis of identified target genes revealed that dFOXO and Kr-h1 co-regulate a large set of metabolic genes, especially those involved in sphingolipid andglycerolipid metabolism. Our results provide addition evidence supporting the notion that cellular metabolic processes are coordinately regulated by diverse transcriptional programs.