Diapausing eggs are a critical life-history stage in rotifers, serving as dispersal units and enabling population persistence under adverse conditions. Despite their ecological significance, the factors shaping their phenotypic variation and the genetic basis of this variation remain largely unexplored. This study pursues the phenotypic characterization of traits potentially related to dispersal in diapausing eggs of two cryptic rotifer species, Brachionus plicatilis and Brachionus rotundiformis. We also examined intraspecific variation in these traits by comparing clones of B. plicatilis derived from floating and sinking diapausing eggs, which may reflect different dispersal strategies. Specifically, we quantified traits related to egg and embryo size, shape, internal structure, weight and lipid content. Additionally, we performed a genome-wide association study (GWAS) in B. plicatilis to identify genetic variants associated with key dispersal-related traits. Significant differences in the phenotypic characterization of the diapausing eggs were found between the two rotifer species: B. plicatilis produced larger and heavier diapausing eggs, while B. rotundiformis exhibited higher lipid content. Broad-sense heritability indicated stronger genetic control of most traits in B. plicatilis, whereas lipid area showed higher heritability in B. rotundiformis. Differences between floating and sinking diapausing eggs in B. plicatilis were linked to lipid content. Floating eggs displayed significantly higher lipid reserves. Genomic analyses identified SNPs significantly associated with embryo area, egg weight, and lipid content, located near genes involved in morphogenesis, embryo development and a protein family that forms gap junctions. This study represents one of the first GWAS applications targeting diapausing egg traits in aquatic microinvertebrates and provides insights into the genetic architecture governing dispersal strategies in rotifers.