BACKGROUND: The MAPK signaling proteins are involved in many eukaryotic cellular processes and signaling networks. However, specific functions of most of these proteins in vertebrate development remain elusive because of potential redundancies. For instance, the upstream activation pathways for ERK1 and ERK2 are highly similar, and also many of their known downstream targets are common. In contrast, mice and zebrafish studies indicate distinct roles for both ERKs in cellular proliferation, oncogenic transformation and development. A major bottleneck for further studies is that relatively little is known of in vivo downstream signaling specific for these kinases. RESULTS: Microarray based gene expression profiling of ERK1 and ERK2 knockdown zebrafish embryos at various stages of early embryogenesis resulted in specific gene expression signature sets that showed pronounced differences in gene ontology analyses. In order to predict functions of these genes, zebrafish specific in silico signaling pathways involved in early embryogenesis were constructed using the GenMAPP program. The obtained transcriptome signatures were analyzed in the BMP, FGF, Nodal and Wnt pathways. Predicted downstream effects of ERK1 and ERK2 knockdown treatments on key pathways responsible for mesendoderm development were confirmed by whole mount in situ hybridization experiments. CONCLUSION: The gene ontology analyses showed that ERK1 and ERK2 target common and distinct gene sets, confirming the difference in knockdown phenotypes and diverse roles for these kinases during embryogenesis. For ERK1 we identified specific genes involved in dorsal-ventral patterning and subsequent embryonic cell migration. For ERK2 we identified genes involved in cell-migration, mesendoderm differentiation and patterning. The specific function of ERK2 in the initiation, maintenance and patterning of mesoderm and endoderm formation was biologically confirmed.