We provide solid phylogenetic evidence that the enigmatic green seaweed order Palmophyllales together with the unicellular planktonic Prasinococcales form the deepest-branching clade of the Chlorophyta. Species of Palmophyllales typically grow in deep marine waters, and are characterized by a unique form of multicellularity, forming macroscopic plants that are composed of isolated and undifferentiated spherical cells embedded in an amorphous gelatinous matrix. Our phylogenetic results alter our understanding of morphological evolution in the green algae. Until present, the early-diverging lineages of the Chlorophyta (the prasinophytes) were only known to include unicellular planktonic algae. Our results point to an independent origin of macroscopic growth and multicellularity outside of the core Chlorophyta. Our study also contributes to a better understanding of plastid genome evolution in green plants. The small, compact and intronless chloroplast genome of Verdigellas peltata (Palmophyllales) shows striking similarities in gene content and organization with the cpDNAs of Prasinococcales and the streptophyte Mesostigma viride, indicating that cpDNA architecture has been extremely well conserved in these deep-branching lineages of green plants. The phylogenetic distinctness of the Palmophyllales-Prasinococcales clade, characterized by unique ultrastructural features, warrants recognition of a new class of green plants, Palmophyllophyceae class. nov.