Plant mitochondrial genomes are often difficult to assemble because of frequent recombination mediated by repeats. Only a few mitochondrial genomes have been characterised in subfamily Papilionoideae of Leguminosae. Here, we report the complete mitochondrial genome of Castanospermum australe A.Cunn. & C.Fraser, an important medicinal and ornamental species in the Aldinoid clade of Papilionoideae. By mapping paired-end reads, seven hypothetical subgenomic conformations were rejected and two hypothetical complete isometric mitochondrial genome conformations that differed by a 64-kb inversion were strongly supported. Quantitative assessment of repeat-spanning read pairs showed a major conformation (MC1) and a minor conformation (MC2). The complete mitochondrial genome of C. australe was, thus, generated as 542 079 bp in length, with a high depth of coverage (∼389.7×). Annotation of this mitochondrial genome yielded 58 genes encoding 37 proteins, 18 tRNAs and three rRNAs, as well as 17 introns and three medium-sized repeats (133, 119 and 114 bp). Comparison of 10 mitochondrial genomes from Papilionoideae demonstrated significant variation in genome size, structure, gene content and RNA editing sites. In addition, mitochondrial genes were shown to be potentially useful in resolving the deep relationships of Papilionoideae.