Pinus merkusii Jungh & De Vries. has become increasingly gathered more attention from researchers because the plant has a range of folk medicinal uses. Heartwood plant is the major source of dehydroabietic acid (DHAA) and abietic acid (AA), which possesses several medicinal properties, such as antiviral, antimicrobial, antiobesity and anti-inflammatory. The research proposed herein a low-cost, fast, specific, uncomplicated, sensitive, precise reverse-phase high-performance liquid chromatography (RP-HPLC). This method was conducted and validated for evaluating an amount of DHAA and AA in ethanol extract and oral spray containing P. merkusii heartwood extract. Additionally, stability and antimicrobial activities against clinically isolated Streptococcus mutans of the oral spray were determined. The separation was achieved on Pursuit 200Å PFP column, 150 × 4.6 mm, particles of 3 µm with a flow rate of 1.0 mL min−1. Methanol and water (70:30 v/v) were used as eluent with an isocratic mode and sample analysis volume was set at 10 µL, at a detection wavelength of 210 and 245 nm. The developed HPLC method for analysis of DHAA and AA showed good linearity with correlation coefficients equal to 1. Moreover, other validation parameters, comprised of accuracy, precision, specificity and detection and quantitation limits of this method displayed excellent reliability, validity and sensitivity. This method could be an interesting alternative for quantitative measurement of P. merkusii heartwood extract, oral spray formulation and other P. merkusii heartwood extract preparations. The result from antibacterial tests suggested that the oral spray containing P. merkusii heartwood extract is able to inhibit the oral pathogens causing dental caries. The oral spray decreased S. mutans population size by about 0.5–2 Log CFU mL−1 at 1–4 h and complete elimination of all bacteria strains within 24 h. This study provides validity for using P. merkusii heartwood extract as an alternative for preventing and treating oral infectious diseases.