The mouse embryo is the canonical model for mammalian preimplantation 
development. Recent advances in single cell profiling allow detailed analysis of 
embryogenesis in other eutherian species, including human, to distinguish 
conserved from divergent regulatory programs and signalling pathways in the 
rodent paradigm. Here, we identify and compare transcriptional features of 
human, marmoset and mouse embryos by single cell RNA-seq. Zygotic genome 
activation correlates with the presence of polycomb repressive complexes in all 
three species, while ribosome biogenesis emerges as a predominant attribute in 
primate embryos, supporting prolonged translation of maternally deposited RNAs. 
We find that transposable element expression signatures are species, stage and 
lineage specific. The pluripotency network in the primate epiblast lacks certain 
regulators that are operative in mouse, but encompasses WNT components and genes 
associated with trophoblast specification. Sequential activation of GATA6, SOX17 
and GATA4 markers of primitive endoderm identity is conserved in primates. 
Unexpectedly, OTX2 is also associated with primitive endoderm specification in 
human and non-human primate blastocysts. Our cross-species analysis demarcates 
both conserved and primate-specific features of preimplantation development, and 
underscores the molecular adaptability of early mammalian embryogenesis.