AbstractThe inheritance patterns of rust resistance genes and molecular markers in microspore‐derived populations of flax were investigated. Plants were produced from anther culture of F1 plants from two crosses. Microspore‐derived plants in anther culture of flax were identified using molecular markers. Two rust resistance genes and three out of six molecular markers were inherited in expected Mendelian ratios in microspore‐derived populations. Distorted segregation for the other three molecular markers was shown to be the result of over‐representation of genomic fragments from the more responsive parent in the F1 donor plant. The implication of this study in relation to androgenesis and flax breeding using anther culture is discussed.