The “good genes” hypothesis for the evolution of male secondary sexual traits poses that female preferences for such traits are driven by indirect genetic benefits. However, support for the hypothesis remains ambiguous, and, in particular, the genetic basis for the benefits has rarely been investigated. Here, we use semi-natural populations of Trinidadian guppies to investigate whether sexually selected traits (orange, black and iridescent colouration, gonopodium length and body size) predict fitness measured as the number of grandoffspring, a metric that integrates across fitness components and sexes. Furthermore, we tested whether two potential sources of genetic benefits – major histocompatibility complex (MHC) genotypes and multilocus heterozygosity (MLH) – are significant predictors of fitness and of the size of sexually selected traits. We found a significant, non-linear effect of the area of black pigmentation and male body size on the number of grandoffspring, suggesting stabilising selection on black area, and non-linear selection favouring small body size. MLH was heritable (h² = 0.14) and significantly predicted the number of grandoffspring, indicating the potential for genetic benefits based on heterozygosity. We also found support for local heterozygosity effects, which may reflect a non-even distribution of genetic load across the genome. MHC genotype was not significantly associated with any tested fitness component, or with the load of Gyrodactylus parasites. Neither MHC nor MLH was a significant predictor of sexually selected traits. Overall, our results highlight the role of heterozygosity in determining fitness but do not provide support for male sexually selected traits being indicators of genetic quality. 

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