Background <p>The evolution of differences in gamete size and number between sexes is a cornerstone of sexual selection theories. The green macroalga <i>Ulva</i>, with incipient anisogamy and parthenogenetic gametes, provides a unique system to investigate theoretical predictions regarding the evolutionary pressures that drive the transition from isogamy to anisogamy, particularly in relation to gamete size differentiation and sexual selection. Its minimal gamete dimorphism and facultative parthenogenesis enable a rare window into early evolutionary steps toward anisogamy.</p> Results <p>By analyzing the expression profiles of sex-biased genes (SBGs) during gametogenesis, we found that SBGs evolve faster than unbiased genes, driven by higher rates of non-synonymous substitution (d<i>N</i>), indicating that SBGs are under stronger selective pressures. Mating type minus-biased genes (<i>mt-</i>BGs) exhibit higher d<i>N</i>/d<i>S</i> values than mating type plus-biased genes (<i>mt+</i>BGs), suggesting stronger selective pressures on <i>mt-</i>BGs, although this difference was not statistically significant (<i>P</i> = 0.08). Using branch-site and RELAX models, we found positive selection and relaxed purifying selection acting on a significant proportion of SBGs, particularly those associated with flagella function.</p> Conclusions <p>This study highlights the selective pressures shaping anisogamy and provides insights into the molecular mechanisms underlying its evolution. The faster evolution of SBGs, particularly <i>mt-</i>BGs, and the positive selection on genes associated with motility, such as those related to flagella function, suggest the importance of enhanced gamete motility in the transition to anisogamy. These findings contribute to our understanding of sexual selection and the evolutionary forces that drive the differentiation of gamete size and number between sexes.</p>