The negative effect of soil pathogens on seedling survival varies considerably among conspecific individuals, but the underlying mechanisms are largely unknown. For variation between heterospecifics, a common explanation is the Janzen-Connell effect: negative density dependence in survival due to specialized pathogens aggregating on common hosts. We test whether an intraspecific Janzen-Connell effect exists, i.e., whether the survival chances of one population's seedlings surrounded by a different conspecific population increase with genetic difference, spatial distance, and trait dissimilarity between them. In a shade-house experiment, we grew seedlings of five populations of each of two subtropical tree species (Castanopsis fissa and Canarium album) for which we measured genetic distance using intersimple sequence repeat (ISSR) analysis and eight common traits/characters, and we treated them with soil material or soil biota filtrate collected from different populations. We found that the relative survival rate increased with increasing dissimilarity measured by spatial distance, genetic distance, and trait differences between the seedling and the population around which the soil was collected. This effect disappeared after soil sterilization. Our results provide evidence that genetic variation, trait similarity, and spatial distance can explain intraspecific variation in plant-soil biotic interactions and suggest that limiting similarity also occurs at the intraspecific level.