Rice tungro is one of the most economically damaging virus diseases in the Philippines, which is caused jointly by Rice tungro bacilliform virus (RTBV) and Rice tungro spherical virus (RTSV). The disease causes a significant effect on rice propagation and cultivation. This study aimed to determine the level of genetic diversity of RTBV coat protein gene sequences collected from tungro-hotspot areas in the Philippines and infer their phylogenetic relationships. A total of 144 RTBV coat protein gene sequences were analyzed from six provinces with 21 municipalities representing Luzon, Visayas, and Mindanao. The highest percentage of RTBV detected was in Camarines Sur at 78% while Nueva Ecija had the least at 45%. Among the provinces, nucleotide diversity and number of segregating sites of RTBV were highest in Camarines Sur (π = 0.010797, S = 145) and lowest in Laguna (π = 0.006233, S = 67). Phylogenetic analysis revealed six divergent groups but did not completely reflect geographical origin while principal coordinate analysis (PCoA) resulted in three major groups: Laguna, Negros Occidental, and Nueva Ecija (Luzon and Visayas); and Camarines Sur and North Cotabato plus Isabela (Luzon and Mindanao). These results could infer genetic differentiation is relevant that disease severity variation could be observed including some breaking in resistance in some areas. There is a need to re-design breeding such as location-specific breeding for RTBV-resistant rice varieties that would consider genetic variation within and between location. Other molecular approaches such as the use of next-generation sequencing could be recommended to support the findings from this study.