The original semigametic line, 57-4, was isolated as a doubled haploid found in the commercial cultivar Pima S-1. The two genotypes were considered to be isogenic for the comparative studies. Although the selfed 57-4 and its derived semigametic line (Sev7) with virescent gene (v7) were consistent in producing haploids in 1996 and 1997, ranging from 36.1% to 49.9%, variation did exist in haploid percentage among individual plant progenies. The semigametic lines produced a substantial number of smaller seed than normal cottons, resulting in greater seed weight variation. The seed weight and haploid percentage are significantly correlated, i.e. the smaller the seed, the more haploid plants produced. Seed less than 100 mg produced all haploid plants. In comparison with Pima S-1, with the use of mRNA differential display technique, thirty-one differentially displayed cDNA fragments were isolated, of which, some exhibited semigamy specific expression across ovules and/or anthers. So far six cDNAs have been cloned and sequenced, one of which showed high homology to a kinetochore protein gene. The comparative molecular studies between semigametic lines and their non-semigametic isolines may eventually lead to the isolation of the semigamy gene.