AbstractThe spontaneous mutation rateµis a crucial parameter to understand evolution and biodiversity. Mutation rates are highly variable across species, suggesting thatµis susceptible to selection and drift and that species life cycle and life history may impact its evolution. In particular, asexual reproduction and haploid selection are expected to affect the mutation rate, but very little empirical data are available to test this expectation. Here, we sequence 30 genomes of a parent–offspring pedigree in the model brown algaEctocarpussp.7, and 137 genomes of an interspecific cross of the closely related brown algaScytosiphonto have access to the spontaneous mutation rate of representative organisms of a complex multicellular eukaryotic lineage outside animals and plants, and to evaluate the potential impact of life cycle on the mutation rate. Brown algae alternate between a haploid and a diploid stage, both multicellular and free living, and utilize both sexual and asexual reproduction. They are, therefore, excellent models to empirically test expectations of the effect of asexual reproduction and haploid selection on mutation rate evolution. We estimate thatEctocarpushas a base substitution rate ofµbs= 4.07 × 10−10per site per generation, whereas theScytosiphoninterspecific cross hadµbs= 1.22 × 10−9. Overall, our estimations suggest that these brown algae, despite being multicellular complex eukaryotes, have unusually low mutation rates. InEctocarpus, effective population size (Ne) could not entirely explain the lowµbs. We propose that the haploid–diploid life cycle, combined with extensive asexual reproduction, may be additional key drivers of the mutation rate in these organisms.