Many reports have revealed that the abundance of microalgae in shrimp ponds vary with changes in environmental factors such as light, temperature, pH, salinity and nutrient level throughout a shrimp culture period. In this study, shrimp cultivation period was divided into three stages (initial = week 0-5, mid = week 6-10 and final = week 11-15). Physical and chemical parameters throughout the cultivation period were studied and species composition of microalgae was monitored. Physical parameters were found to fluctuate widely with light intensity ranging between 182.23-1278 μmol photon m(-2)s(-1), temperature between 29.56°C -31.59°C, dissolved oxygen (DO) between 4.56-8.21 mg/l, pH between 7.65-8.49 and salinity between 20‰-30‰. Ammonium (NH4 (+)-N), nitrite (NO2 (-)-N), nitrate (NO3 (-)-N), and orthophosphate (PO4 (3-)-P) concentrations in the pond at all cultivation stages ranged from 0.017 to 0.38 mg/l, 0.24 to 2.12 mg/l, 0.06 to 0.98 mg/l and 0.16 to 1.93 mg/l respectively. Statistical test (ANOVA) showed that there were no significant difference (p<0.05) in nutrients concentrations among the cultivation stages. All nutrients concentrations however were still in the tolerable level and safe for shrimp culture. The chlorophyll a contents were found to range from 5.03±2.17 to 32.61±0.35 μg/l throughout the cultivation period. A total of 19 microalgae species were found in the shrimp pond, with diatoms contributing up to 72% of the species followed by Chlorophyta (11%) and Cyanophyta (11%). However, weekly species abundance varied through the study period. At the initial stage, when there were no shrimps in the pond, Anabaena spp. and Oscillatoria spp. (Cyanophyta) were the dominant species, followed by Chlorella sp. and Dunaliella sp. (Chlorophyta). When shrimps were introduced into the pond, Amphora sp., Navicula sp. Gyrosigma sp. and Nitzschia sp. (diatoms) started to exist. At the middle and towards the final stage of the shrimp culture period diatoms were the dominant species. The Chlorophyta (Chlorella sp.) domination took place only twice, which was at week 2 and 13. The absence of some of the coastal water microalgae species in the shrimp pond was most likely due to the fact that they could not tolerate the physicochemical factors of harsh environment. In this study, Cylindrotheca closterium was regarded as the most tolerant species among the microalgae due to its ability to exist for 6 weeks out of the 15 weeks of cultivation.