Forest structure, fuel characteristics, and fire regimes of mixed conifer forests in the Western United States (US) have been dramatically altered since the early 20th century. Fuel treatments have been suggested as a means to limit the size and intensity of wildfires but few experiments are available to analyze the ecological effects of different treatments. The objective of this study is to determine how mechanical, prescribed fire, and mechanical and fire combination fuel treatments affected seedling density by species in a Sierra Nevada mixed conifer forest. The relative influences of stand-level light availability and substrate quality on conifer and black oak seedling densities are assessed. For all species combined, seedling densities increased when the fire only treatment was applied and no change was detected for the other treatments. The fire only treatment as well as the combined fire plus mechanical treatment had the effect of significantly increasing Douglas-fir seedling density. Ponderosa pine seedling densities significantly increased when the fire plus mechanical treatment was applied. California black oak seedling density decreased when the fire only treatment was applied but no change was detected for the other treatments. Previous studies have found a decline in sugar pine and ponderosa pine in dense stands of Sierran mixed conifer forests. The findings reported here corroborate these studies in that current conditions are not conducive to recruitment of ponderosa pine and sugar pine species. Our initial results indicate, that in this case, treatments used to reduce fire hazard may not result in retention or recruitment of California black oak and sugar pine seedlings.