The temporal variation in the taxonomic distinctness of biofilm-associated diatom microflora within the colonization process was studied in coastal waters of the Yellow Sea, northern China from May to June 2014. Samples were collected at depths of 1 and 3 m, using glass slides as an artificial substratum. The colonization dynamics of diatom microflora showed similar species composition at both depths. In the young communities (1–7 days), the taxonomic patterns showed high variability compared with those in the mature ones (10 days and more). However, taxonomic distinctness indices at the two depths differed during early stages (e.g. 1–3 days). The taxonomic diversity (Δ) represented a high variability (coefficients of variation >10%) over all colonization periods, whereas the taxonomic distinctness (Δ*), average taxonomic distinctness (Δ+) and variation in taxonomic distinctness (Λ+) showed high stability (coefficients of variation <10%) after 7 days. Based on these findings, we suggest that the exposure time of more than 7 days may be sufficient to identify the taxonomic distinctness of biofilm-associated diatom microflora for both community research and monitoring programmes in marine ecosystems.