Cambrian preservation of fossilized tissues provides crucial information about divergent cerebral arrangements amongst stem arthropods. One such genus isMollisonia, whose clustered appendages beneath a frontal carapace suggest an early chelicerate. Here we apply neuroanatomical, genetic, and developmental analysis to curated fossil data ofMollisoniato demonstrate that instead of a linear organization of seriate parts like in other Cambrian arthropods, theMollisoniabrain is folded back over segmental ganglia of the prosoma, an organization characterizing the brains of all modern arachnids. The unexpectedly early acquisition of this apomorphic character state demonstrates the divergence of marine Arachnida represented byMollisoniafrom Merostomata (horseshoe crabs) and its sister group Pycnogonida (sea spiders), both of which have linearly organized cerebra. While fossil evidence supports a marine origin of total group Chelicerata, we show Mollisoniidae defining the base of the arachnid tree of life that excludes Merostomata and Pycnogonida.