Enzyme electrophoresis was used to compare the isozyme phenotypes of Oryza sativa, IR31917 (AA genome), and two O. minuta accessions (Om 101089 and Om101141; BBCC genome) for ten enzyme systems. Between the two species, two systems were monomorphic (isocitrate dehydrogenase and alcohol dehydrogenase) and eight were polymorphic (shikimate dehydrogenase, phosphogluconate dehydrogenase, phosphoglucose isomerase, malate dehydrogenase, glutamate oxaloacetate transaminase, esterase, aminopeptidase, and endopeptidase). Polymorphism between O. minuta accessions was detected for shikimate dehydrogenase and glutamate oxaloacetate. As expected, the quaternary structure of the O. minuta isozymes was comparable to that of O. sativa. Possible allelic relationships with known O. sativa alleles and their genomic designation are discussed. Combined with chromosome data, the interspecific variation was exploited to monitor the relative genetic contribution of the two parents in the IR31917/Om101141 F1 hybrids and recurrent (IR31917) backcross progenies. The isozyme content of F1 hybrid reflected its triploid nature (ABC genome composition), while that of the backcross progenies paralleled the duplication of the A genome and the gradual loss of O. minuta chromosomes during the backcrossing process. Evidence is provided for a degree of homoeology between the A, B, and C genomes, and for introgression from O. minuta into O. sativa.