Fifty-three sugarcane accessions from Aklan, Iloilo, Cagayan, Nueva Vizcaya, Isabela, and Bohol were characterized using forty-two morphometric parameters and forty microsatellite markers. Twenty-six morphological characters using the Shannon-Weaver diversity index showed high variability (H’ = > 0.76) and were able to characterize the fifty-three sugarcane accessions. Cluster analysis of morphological traits based on sequential agglomerative hierarchical test and Euclidean distance revealed two groupings at 0.3 coefficient of dissimilarity. The clustering of some accessions was irrespective of their geographical origin indicating a high degree of phenotypic similarity in some accessions. Out of the forty microsatellite markers, twenty-five (63%) have a PIC value greater than 0.5 with Sach 53 showing the highest at 0.89. This implies that these markers are suitable for sugarcane genetic diversity studies as they can detect a high number of discernable alleles. Molecular cluster analysis generated using Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Jaccard distance showed two clusters at 0.4 coefficient of dissimilarity. In cluster I, twenty-one accessions from Aklan and Iloilo grouped indicating genetic similarity. Aklan and Iloilo provinces are both located in the same geographic island in Western Visayas, hence, the observed grouping in cluster I. On the other hand, thirty-two sugarcane accessions from Northern Luzon (Cagayan, Nueva Vizcaya, and Isabela), Iloilo, Aklan, and Bohol were grouped in cluster II. The observed clustering of accessions from different regions implies the extensive distribution of sugarcane germplasm to the different parts of the Philippines.