In order to understand molecular basis of heterosis, mRNA differential display was used to analyze the differences in gene expression between seeds of 18 reciprocal hybrids and their 6 parents at 6th day after pollination. The relationship between gene expression patterns and heterosis was determined. Only bands that can be repeated in duplicate PCR were used for analysis so as to reduce false positive bands. Among the total of 2,025 bands displayed, 1,386 bands (68.43%) were reproducible. Eight patterns (fifteen kinds) of gene expression were observed, which include: (1) bands occurring in only one parent (two kinds); (2) bands observed in both hybrids and one parent (two kinds); (3) bands detected in parents and one hybrid (two kinds); (4) bands displayed in only one hybrid (two kinds); (5) bands revealed in one hybrid and its corresponding female (two kinds) or male (two kinds) parent; (6) bands visualized in only both hybrids (one kind); (7) bands occurring in only parents (one kind); (8) bands observed in parents and both hybrids (one kind). Our results indicate that differences of gene expression between hybrids and their parents are very obvious. The percentages of bands observed in only both hybrids and in only both parents are lower. The analysis shows that bands observed in parents and both hybrids are not correlated with all nine agronomic traits, which indicates differentially expressed genes are mainly responsible for the observed heterosis. At least one pattern of differential gene expression is significantly correlated with nine agronomic traits. Silenced bands in hybrid (which include bands occurring in only one parent, bands detected in both parents and one hybrid and bands in only parents) and bands present in one hybrid and its corresponding female or male parent are likely to play important roles in heterosis. These results suggest that early seed development could be closely related to heterosis.