The goal of this study was to examine and assess the stability of phytoplankton communities in connection to the different health status type of shrimp pond (healthy and diseased) in an intensive culture. The research was conducted in two ponds located in Probolinggo region, which had different health status until eight week of harvest period. Several water quality variables and phytoplankton community composition were observed. Non-metric dimensional scaling and analysis of similarity were used to compare the phytoplankton community structure and water quality parameters in both ponds. In addition, stability of phytoplankton community in these ponds were measured using species turnover rate, rate change of composition community, and community stability indices. The results showed that phytoplankton community structure and water quality factors between diseased and healthy pond were not statistically significant. On the other hand, the phytoplankton community in healthy pond was more stable than that of diseased pond. Furthermore, ammonia and phosphate were found as the dominant factors affecting phytoplankton community in the studied ponds.