Pou5f1/Oct4 is a transcription factor required for pluripotency of embryonic stem cells in mammals. Zebrafish pou5f1 deficient maternal and zygotic spiel ohne grenzen (MZspg) mutant embryos develop severe gastrulation defects, are dorsalized, and defective in endoderm formation. Here we analyze in detail gastrulation defects, which are manifested by a severe delay in epiboly progression. All three embryonic lineages in MZspg embryos behave abnormally during epiboly: the yolk cell forms an altered array of cortical microtubules and F-Actin, with large patches of microtubule free areas; the enveloping layer (EVL) is delayed in the coordinated cell shape changes of marginal cells, that may be mediated by F-Actin; the deep layer cells (DEL), forming the embryo proper, are non-autonomously affected in their motility and do not enter the space opening by epiboly of the EVL. Analysis of adhesiveness as well as high resolution in vivo time lapse image analysis of DEL cells suggests changed adhesive properties and inability to migrate properly on EVL and yolk syncytial layer (YSL) surfaces. Our data further reveal that during epiboly the EVL may actively probe the YSL by filopodia formation, rather than just being passively pulled vegetalwards. Our findings on the effect of Pou5f1 on cell behavior may be relevant to understand stem cell behavior and tumorigenesis involving Pou5f1.