The increase in honey fraud in the global market has highlighted the importance of pollen analysis in determining or confirming the botanical and geographical origins of honey. Numerous studies are currently underway to develop efficient and rapid methods for the determination of the quality, botanical, and geographical origin of honey. Typically, the physicochemical analysis of honey is used to evaluate its quality and geographical source. In this study, flow cytometry, a technique extensively employed in immunology and hematology, was first applied to analyze and characterize pollen from longan honeys from Taiwan and Thailand. The flow cytometry was employed for forward scatter (FSC), side scatter (SSC), Y610-A, and NUV450 to analyze longan honey samples from Taiwan and Thailand. Taiwan’s longan honeys were rich in pollens; however, based upon the FSC and SSC analyses, the pollens from Thai longan honeys were larger and more granular. The Y610/20 emission area was greatest in Thai pollens. The NUV450 measured in the near UV laser was also greater in Thai pollen. Additionally, honey samples were also analysed for physiochemical properties including moisture content, pH, ash content, viscosity, and hydroxymethylfurfural (HMF) for physiochemical properties of longan honey samples from both countries. The moisture content of honey from Taiwan varied between 20.90% and 23.40%, whereas honey from Thailand ranged from 19.50% to 23.50%. A total of 60% of Taiwan’s longan honey was found to have a dark amber color, and only 20% of Thai longan honey exhibited a dark amber color. Furthermore, the pH range of honey from Taiwan was found to be between 4.00 and 4.16, and the pH of Thai honey ranged from 4.01 to 4.12. The ash content of honey samples from Taiwan ranged from 0.05% to 0.23%, and Thai honey had a range of 0.01% to 0.9%. All samples were negative for the Fiehe’s test, indicating the absence of HMF. This analysis lays the groundwork for rapid identification the origins of the honey, applying flow cytometry in conjunction with physicochemical analysis to assess its quality.