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The present study was conducted to investigate the relationship between parental molecular marker diversity and hybrid performance in both intra- and interspecific hybrids of cotton to evaluate the feasibility of predicting hybrid performance using molecular markers. Three cytoplasmic male sterile (CMS) lines were crossed with 10 restorer lines to produce 22 F 1 hybrids during 2003. Of 22 F 1 s, 14 hybrids were intraspecific (Gossypium hirsutum x G. hirsutum) and eight interspecific (G. hirsutum x G. barbudense). These 22 F 1 hybrids and their parents were evaluated for yield and fibre quality traits at Zhejiang University, Hangzhou, China during 2004 and 2005. Genetic distances (GD) among the parents were calculated from 56 random-amplified polymorphic DNAs (RAPD) and 66 simple sequence repeat (SSR) marker data, and their correlation with hybrid performance and heterosis were analysed. The parents could be discriminated into G. hirsutum and G. barbadense clusters by cluster analysis based on both RAPD and SSR markers data. The correlation (r = 0.503, P≤0.05) was calculated between GD rapd (GD based on RAPD markers) and GD ssr (GD based on SSR markers). Correlation of GD with hybrid performance and heterosis differed considerably between intra- and interspecific hybrids. The correlation between GD and hybrid performance was non-significant for most of traits within the hybrids of G. hirsutum species. However, it was significantly and positively correlated for fibre length, fibre strength and elongation in interspecific hybrids. The relationship between GD and heterosis was observed to be positively significant for boll weight within hybrids of G. hirsutum with significant and negative correlations for fibre length and elongation. In conclusion, the power of predicting hybrid performance using molecular markers in cotton is low. But, the relationship between SSR marker heterozygosity and hybrid performance can be used to predict fibre length during interspecific hybrid cotton breeding.