Hox collinearity - the temporal and spatial expression of Hox genes according to their sequential order in the genome - has been implicated in the establishment of the body plan. However, the mechanisms by which Hox genes interconnect the spatial and temporal regulation of cell behaviours in early embryonic development are not fully understood. Here, Moriyama and colleagues show that Hoxb genes are expressed in a temporally collinear manner at the zebrafish embryo margin, which results in spatial collinearity along the body axis during gastrulation. Firstly, through morpholino knockdown studies and generation of loss-of-function mutants, they find that perturbing early (or anterior) Hoxb genes severely disrupts the timely ingression of mesodermal and endodermal (mesendodermal) progenitor cells, which is important for the positioning of cells along the anterior-posterior body axis. Additionally, premature or ectopic expression of late (or posterior) Hoxb genes suppresses cell ingression. Using transplantation assays and 4-dimensional imaging, they also show that Hoxb genes upregulate cell blebbing of mesendodermal cells at the embryo margin that precedes successful cell ingression. Overall, this work reveals that spatiotemporally ordered expression of Hoxb genes regulates dynamic cell surface fluctuations during early gastrulation.