Low seed set, owing to partial incompatibility, can limit sexual gene transfer and haploid production efficiency in wide crosses. The inheritance of partial incompatibility in barley Hordeum vulgare L. × H. bulbosum L. crosses and its effect on gamete sampling in doubled haploid production were studied by doubled haploid progeny analysis. The dominant, monogenic control of partial incompatibility in 'Vada' was confirmed. Partial incompatibility in 'Harrington' is also monogenic but appears to be controlled by a different gene. An association between the Inc gene and a deficiency in a stigma–stylodium specific high pI protein was found in the co-segregation analysis of doubled haploid progeny. Segregation analysis of Mendelian markers in doubled haploid progeny showed that there is no evidence that the compatibility status of the parents has an effect on gamete sampling by the bulbosum technique.Key words: barley, haploids, Hordeum bulbosum, incompatibility.