Ecological studies of contaminating microzooplankton in microalgal mass culture are important for large-scale cultivation risk management and remediation strategies, with the ultimate goal to ensure the sustainable high-yield production of microalgal biomass. Using multivariate statistical techniques, the characteristics and relationships with environmental variables of contaminating microzooplankton species were studied in commercial production of Spirulina platensis in outdoor raceway ponds in East and North China. A total of 16 microzooplankton species were identified from 64 large-scale raceway ponds, including three rotifers, two amoebae, and eleven ciliates. The relative abundance of individual microzooplankton species was in an order, from high to low, of ciliates > rotifers > amoebae. The ciliate Cyclidium marinum was the most frequently occurring species, mainly due to its wide tolerance of environmental conditions; and the rotifer Brachionus plicatilis was the key contaminating species, responsible for major loss of biomass productivity owing to its high level of occurrence and feed characteristics as an algivore. The high salinity habitats of the culture systems in North China featured the ciliate Frontonia didieri as an algophagous indicator species, while in East China the amoebae Nuclearia simplex and Euplaesiobystra hypersalinica were indicators for seed ponds and production ponds, respectively, attributed to the specific physicochemical conditions of the local environments. Fine tuning of salinity and pH away even temporarily from the optima of these contaminating microzooplankton species may be an easy and effective protocol for contamination control. Our investigation indicates the importance of comprehensively considering the environmental optima, tolerances and feed characteristics of contaminating species, together with continuous monitoring and ecological data analysis, for efficient management strategies geared towards the mitigation of biological contamination in microalgal mass culture. (C) 2016 Elsevier B.V. All rights reserved.