Colonization features and taxonomic relatedness measures of ciliate communities have been used as useful indicators for marine bioassessment. The influence of enumeration time periods on analyzing colonization features measures of periphytic ciliate communities was studied in coastal waters of the Yellow Sea, northern China, during the period of May-June 2010. Ciliated protozoan samples were collected at depths of 1 m using an artificial substratum and were analyzed with different enumeration schemes. The ciliate species were identified using living observation and silver impregnation. Data analyses were conducted using a range of multivariate statistical routines. Enumeration time periods represented a strong influence on analyzing both colonization and taxonomic relatedness features of periphytic ciliate communities, although no significant changes occurred in colonization patterns between two enumeration schemes (within 24 and 24-48 h after sampling). The delayed enumeration (within 24-48 h) may result in the species richness, individual abundance, colonization rate decreasing to standard errors of >10 % in samples with almost all colonization ages, and in the similarities of the communities being reduced to 11-38 %. However, the species biodiversity (e.g., species diversity and evenness, except species richness) and taxonomic relatedness (taxonomic diversity, taxonomic distinctness and average taxonomic distinctness, except variation in taxonomic distinctness) measures of periphytic ciliate communities were weakly sensitive to disturbance from the delayed enumeration, achieving standard errors of <10 and <5 % during the colonization periods, respectively. These results suggest that the enumeration should be completed as soon as possible within 24 h after sampling to analyze colonization and taxonomic relatedness features of periphytic ciliate communities, and that the species diversity and taxonomic distinctness measures can be used on a robust bioindicator with weak dependence on enumeration time limits for monitoring programs and ecological investigations in marine ecosystems.