Marine reserves that prohibit fishing often result in greater densities of individuals and more species than adjacent fished areas. However, simple conclusions about their effects on species richness are confounded, because more species are expected to occur wherever there are more individuals. Here, there is an important distinction between the number of species per sampling unit (species density), and species richness measured as the number of species per given number of individuals. When conservation of species richness is an important goal, analyses need to discriminate between the alternative explanations for differences in the number of species. We used rarefaction to test whether species richness was higher in two 'no-take' marine reserves after controlling for differences in the density of individuals. We surveyed each reserve in three different years. There was a higher density of individuals and species in each reserve than in adjacent fished areas. However, rarefaction analyses indicated that effects on species richness were weak after controlling for the number of individuals: slightly higher species richness was recorded inside each reserve in one of three surveys, but the difference was small, and was apparent only when the maximum number of individuals was approached. Our results therefore indicate that patterns in species density were not reflected by patterns in species richness-the application of rarefaction methods is needed to determine the responses of species richness to protection elsewhere. The distinction between species density and species richness will not be important in all situations, but when it is important, inferences about species richness cannot be reliably deduced from measurements of species density.