Scutellaria indica is a perennial herb with both chasmogamous (CH) and cleistogamous (CL) flowers on the same plant in some populations, and only CL flowers in other populations. Actual seed production by CH and CL flowers was investigated in populations of S. indica. The average seed set of CL flowers was 19 times higher than CH flowers, indicating much greater fertilization success. The CL seeds were also significantly heavier than the CH seeds. However, the resource cost of producing a CH flower was much higher than that of producing a CL flower. The CH flower was approximately seven times larger, and its pollen/ovule ratio was approximately five times higher than flowers. The level and pattern of genetic diversity at both allozyme and random amplified polymorphic DNA (RAPD) levels were consistent with a predominantly selfing system in the species. The average amount of within-population genetic variation was extremely low (A = 1.025, P = 2.36%, HO = 0.001 and HE = 0.008 based on allozyme data, and P = 8.94% and HE = 0.03 based on RAPD data). At the species level, the estimates of total gene diversity (HT) were 0. 101 based on allozyme data and 0.139 based on RAPD data. A very high level of genetic differentiation occurred between populations (allozyme GST = 0.92 and RAPD GST = 0.81). Genetic drift coupled with predominant cleistogamous selfing apparently played the major role in determining the population genetic structure in S. indica. Although the features associated with CH and CL flower and seed production seem to be sufficient for the evolution of complete cleistogamy in S. indica, random fixation of alternative alleles for dimorphic or complete cleistogamy in small populations could maintain the multiple strategy of chasmogamous and cleistogamous reproduction in the species.