Recruitment patterns in clonal plant populations are predicted to vary with seed dispersal capability and disturbance regime, such that species with small, widely dispersed seeds will become increasingly dominated by vegetative recruitment on disturbed areas following early colonization. Subsequent mortality due to competitive or stochastic effects is then predicted to cause a gradual decline in both clonal diversity and the ability of surviving clones to avoid geitonogamous mating and possible inbreeding depression. We tested predictions of these hypotheses by comparing four adjacent populations of the salt marsh plant, Spartina alterniflora, ranging in age from 2 to ∼50 yr, by measuring fine‐scale genetic structure at the level of both ramets and genets, and the rate of inbreeding. For this purpose, we sampled maternal tissue and seeds from discrete patches in the field and then genotyped both maternal and seedling tissue (germinated in a growth chamber) using standard molecular protocols. As predicted, we observed an increase in clonal diversity (measured as the complement of the Simpson Index corrected for finite sample sizes, 1 − D) up to a maximum of 0.71 within 3‐m² patches at 16 yr, declining to 0.55 by ∼50 yr. Local recruitment of seedlings was evident as genetic structure occurring at the level of patches, as measured by the fixation index, θ, which was inversely correlated with diversity (R² > 0.90 at all patch scales). Outcrossing rates were positively associated with clonal diversity, with the highest level (89%) at an intermediate level of 1 − D. The greatest selfing (32%) occurred in young (2‐yr‐old) patches with low diversity. Biparental inbreeding was minimal in all populations, never exceeding 1%. Inbreeding depression was inferred to be severe, as evidenced by near‐zero adult inbreeding coefficients. These results suggest a possible fitness trade‐off between clonal growth and the opportunity for outcrossing. We recommend that restoration plantings of clonal species with limited sexual recruitment capabilities should be designed to ensure adequate clonal diversity for the avoidance of inbreeding and the ability to adapt to subsequent environmental disturbances.