A study to investigate the relationship between black flies (Simuliidae)pupaabundanceand physio-chemical parameters such as velocity, water temperature, pH,dissolved oxygen, conductivity and total dissolved solid was conducted at Tambunan district,Sabah. A total of six rivers were selected as sampling stations. Five sampling points locatedat a distance of 5-10 meters were established in each sampling station. Sampling wasconducted every fortnight for a duration of six months from October 2015 until March 2017.Samples of black flies larvae and pupae were manually collected from substrates consistingof grasses, plant roots and plastics which were found stuck in between the rocks withrunning water area. Water quality parameters that were measured during every sampling,include water temperature, velocity, pH, dissolved oxygen, conductivity and total dissolvesolids (TDS). Results from this study showed that The Principal Component Analysis (PCA)revealed two PC’s which had eigenvalues >1.0 and together accounted for 78% totalvariability of the physio-chemical parameters. PC-1 which accounted 56% of variabilitydefined a normal temperature (23-250C), high water velocity, high dissolved oxygen, lowconductivity and low total dissolved solid. While PC-2 explained 22% of the variability wasrelated to water pH. Pearson’s correlation result shows that only velocity had a significantrelationship with the abundance of black flies (r=0.512, p<0.01), while other parameters didnot show any significant relationship with its abundance. In conclusion, results from thisstudy revealed that only water velocity had a significant relationship with the abundance ofblack flies.