Inbreeding is a major component of the mating system in populations of many plants and animals, particularly hermaphroditic species. In flowering plants, inbreeding can occur through self-pollination within flowers (autogamy), self-pollination between flowers on the same plant (geitonogamy), or cross-pollination between closely related individuals (biparental inbreeding). We performed a floral emasculation experiment in 10 populations of Aquilegia canadensis (Ranunculaceae) and used allozyme markers to estimate the relative contribution of each mode of inbreeding to the mating system. We also examined how these modes of inbreeding were influenced by aspects of population structure and floral morphology and display predicted to affect the mating system. All populations engaged in substantial inbreeding. On average, only 25% of seed was produced by outcrossing (range among populations = 9–37%), which correlated positively with both population size (r = 0.61) and density (r = 0.64). Inbreeding occurred through autogamy and biparental inbreeding, and the relative contribution of each was highly variable among populations. Estimates of geitonogamy were not significantly greater than zero in any population. We detected substantial biparental inbreeding (mean = 14% of seeds, range = 4–24%) by estimating apparent selfing in emasculated plants with no opportunity for true selfing. This mode of inbreeding correlated negatively with population size (r = −0.87) and positively with canopy cover (r = 0.90), suggesting that population characteristics that increase outcross pollen transfer reduce biparental inbreeding. Autogamy was the largest component of the mating system in all populations (mean = 58%, range = 37–84%) and, as expected, was lowest in populations with the most herkogamous flowers (r = −0.59). Although autogamy provides reproductive assurance in natural populations of A. canadensis, it discounts ovules from making superior outcrossed seed. Hence, high autogamy in these populations seems disadvantageous, and therefore it is difficult to explain the extensive variation in herkogamy observed both among and especially within populations.