To determine the morphological characteristics of variations in populations of female adult sand fly, Sergentomyia anodontis Quate and Fairchild, 1961 in caves in southern Thailand using morphometric analysis. Methods: A total of 107 female Sergentomyia anodontis were isolated from 651 sand flies captured by CDC light traps overnight in caves in Surat Thani, Nakhon Si Thammarat, Satun and Songkhla provinces from February to December 2017. Measurement of 23 external and internal morphological characteristics was conducted. Data were tested with preliminary statistics (Kolmogorov-Smirnov test, Levene's test and Box's test of equality of covariance matrices) and by one-way ANOVA or Kruskal-Wallis test. Measurements were analyzed using canonical discriminant analysis. Results: There were 11 morphological characteristics with high variability while two characteristics exhibited low variation. The sand fly populations from Nakhon Si Thammarat, Satun and Songkhla provinces were very similar but were separate from that in Surat Thani province based on canonical discriminant analysis data. This indicates that the morphological variation founding is a result of the diversity of habitats in each population and the geographic features of caves in each area, such as their altitude above sea level. Conclusions: There is a certain variation in the morphology of Sergentomyia anodontis sand flies at the population level which may be used for future classification of sand flies.