The B-genome of Glycine subg. Glycine (Leguminosae: Papilionoideae) comprises three named Australian diploid species and a number of distinctive but as yet not formally recognized taxa. Chloroplast DNA restriction site studies of this group revealed a monophyletic set of haplotypes that were polymorphic within taxa and transgressed apparent taxonomic boundaries. We have surveyed over 40 accessions from that study for sequence variation at the single-copy, intron-containing nuclear locus histone H3-D. As expected for these largely inbreeding taxa, there was little evidence of heterozygosity, facilitating direct sequencing of PCR products. A total of 21 alleles were found, differing by as many as 17 nucleotide substitutions in the approximately 500 bp region analyzed. Phylogenetic analysis identified two shortest trees, and revealed very little homoplasy (ci > 0.95). Four major groups of alleles were well-supported in the H3-D trees, those from: 1) G. microphylla; 2) an unnamed but morphologically distinctive taxon supported by cpDNA as basal in the diploid B-genome group (G. sp. aff. G. tabacina); 3) two accessions of a second unnamed taxon from an ecologically distinctive region of high Glycine diversity; and 4) the remaining accessions, including G. latifolia, several unnamed taxa, and the "diploid G. tabacina complex." Several subclades appeared in the fourth group. The distribution of H3-D alleles agreed much better with species boundaries than did the distribution of cpDNA haplotypes. The agreement of H3-D alleles with morphology implicates cpDNA as the incongruent marker, and leaves us with the usual processes--lineage sorting or introgression--as possible explanations, as usual without distinguishing decisively between them. The H3-D data themselves pose some interesting problems, however, such as how there came to be only a single identical allele throughout our geographically broad sample of G. microphylla.

Key words: cpDNA, Glycine, histone gene sequences, incongruence, Leguminosae, phylogeny