Abstract
<title>Abstract</title> <p> Capiz is one of the major coconut-producing provinces in the Visayas, but horti-morphological and molecular characterization of <italic>in situ</italic> coconut populations in the locality remains limited. This study conducted an <italic>in-situ</italic> characterization of the fruit components and yield parameters as well as the genetic diversity and population structure of three tall coconut populations in Capiz using 16 SSR markers. Among these populations, CAP3 (1,543 g) has the highest total fruit weight, followed by CAP2 (1,419 g), while CAP1 (1,238 g) exhibited the lowest fruit weight. Furthermore, CAP3 showed relatively high values in terms of the number of leaves per palm, number of bunches, number of nuts per bunch, and nut yield per palm and per hectare. To complement these horti-morphological findings, SSR analysis revealed a total of 56 alleles, with an average of 3.5 alleles per locus. Observed heterozygosity (Ho = 0.821) exceeded expected heterozygosity (He = 0.658) and PIC values ranged from 0.520 to 0.669. Analysis of molecular variance (AMOVA) revealed that 93% of total genetic variation occurred within populations, while only 7% was distributed among populations. Genetic differentiation among populations was low to moderate but statistically significant (Φ <sub> <italic>ST</italic> </sub> = 0.067; p < 0.001), suggesting a high degree of genetic connectivity and gene flow, overriding the effects of geographic distance between and among sampling sites. Furthermore, hierarchical clustering and principal coordinates analysis (PCoA) showed extensive intermixing of individuals with no clear geographic structuring. Overall, the populations exhibited moderate to high genetic diversity, highlighting their value as genetic resources for future breeding, conservation, and replanting purposes. </p>