Information about histone sequences and histone gene organization from invertebrate chordates is completely lacking. A genomic clone containing linked H3 and H4 histone genes from the urochordate Styela plicata was analyzed. The nucleotide sequence indicates that the two genes are transcribed in opposite directions and have structural similarities to cell cycle-dependent histones. Unique amino acid replacements occur in H3 at positions 88 (serine) and 98 (arginine). In H4, the methionine at position 84 is replaced by a leucine, a replacement found only in fungi. Codon usage patterns are nonrandom and resemble invertebrate patterns. The H3 and H4 genes are polymorphic and are represented five times per haploid genome.