Background <p>White calla lily (<i>Zantedeschia aethiopica</i> L. Spreng) is a perennial ornamental species valued for its distinctive spathe and spadix. Despite its commercial importance, breeding progress is limited by a narrow genetic base, reproductive barriers, and insufficient characterization of available germplasm.</p> Methods and results <p>A total of 102 white calla lily genotypes were evaluated in an alpha-lattice design with three replications using 12 agro-morphological traits across four cropping seasons, along with four molecular marker systems. Significant variation was observed for all traits, and superior genotypes such as G21, G87, and G90 were identified for key floral and yield attributes. Variability parameters, correlation, and principal component analysis indicated that most traits are under strong additive genetic control and suitable for selection. PH, STL, NOL and PL were key determinants of NOFL, while SPL, SPW and SPDW contributed to overall variation. Molecular analysis revealed that SCoT markers exhibited the highest discriminating power, while SSR markers showed higher locus-specific informativeness. Population structure analysis indicated two sub-populations with moderate stratification and admixture among genotypes. PCoA, hierarchical clustering, and tanglegram analysis revealed a continuous distribution with partial clustering and only partial correspondence between phenotypic and molecular groupings.</p> Conclusions <p>The study reveals substantial genetic variability and identifies key plant architectural and floral traits linked to flower yield in white calla lily. The combined use of phenotypic and molecular approaches improves genotype differentiation and highlights the limitations of relying solely on morphological traits. These findings provide a reliable basis for selection and the development of high-yielding, genetically diverse cultivars.</p>