Segregation ratios of allozymes in haploid female gametophytes obtained from viable seed were studied in a natural population of jack pine, Pinus banksiana. Stability of these ratios was assessed for three levels of the sexually reproductive crown as well as for four years of natural fertilization. Analyses of observed segregation ratios of four of five polymorphic isozyme loci showed good correspondence to the overall 1∶1 ratios expected for simple Mendelian inheritance. Allozymes of glucose-6-phosphate dehydrogenase did not segregate in the expected 1∶1 ratio. In addition, there were significant deviations from the expected segregation ratio for all the loci at some sampling positions on individual trees. Heterogeneity of segregation among trees, strata and years could be the result of pollen pool heterogeneity, segregation distortion and/or recessive lethal and semi-lethal gene combinations resulting in early embryo abortion. These types of segregation deviations in viable seed can affect the estimation of allele frequencies from bulked samples of a small number of individuals, the inference of heterozygosity/homozygosity of parental trees, and estimates of selfing rates.