Genetic diversity is a fundamental population genetic parameter, and predicts adaptive capacity. Neutral theory predicts a positive correlation between population (or range) size and genetic diversity, but this can be confounded by other demographic processes. To investigate the role of range size, population fluctuation and introgression in determining genetic diversity, we generate and analyse population-level, genomic-scale SNP data from 21 species of Australian Gehyra geckos (769 samples) that vary in range size over three orders of magnitude. Using a best-practice approach to estimate SNP-based heterozygosity, we found a significantly positive overall correlation between range size and heterozygosity, although with a shallow slope (R² = 0.30), consistent with Lewontin’s Paradox. At a clade level, we show a stronger relationship between range size and heterozygosity in the australis group (R² = 0.74, p < 0.01) than the nana group (R² = 0.15, n.s.). A significantly negative correlation between Tajima’s D and range size in both groups, and evidence for introgression in the nana group, suggest a role for both population fluctuation and introgression in driving deviations from theoretical expectations. Our results provide insight into the biological and demographic processes that influence genetic diversity, in addition to neutral expectations.