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Inconsistency in taxonomic identification and analyst bias impede the effective use of diatom data in regional and national stream and lake surveys. In this study, we evaluated the effect of existing protocols and a revised protocol on the precision of diatom species counts. The revised protocol adjusts four elements of sample preparation, taxon identification and enumeration, and quality control (QC). We used six independent data sets to assess the effect of the adjustments on analytical outcomes. The first data set was produced by three laboratories with a total of five analysts following established protocols (Charles et al., Protocols for the analysis of algal samples collected as part of the U.S. Geological Survey National Water-Quality Assessment, 2002) or their slight variations. The remaining data sets were produced by one to three laboratories with a total of two to three analysts following a revised protocol. The revised protocol included the following modifications: (1) development of coordinated precount voucher floras based on morphological operational taxonomic units, (2) random assignment of samples to analysts, (3) postcount identification and documentation of taxa (as opposed to an approach in which analysts assign names while they enumerate), and (4) increased use of QC samples. The revised protocol reduced taxonomic bias, as measured by reduction in analyst signal, and improved similarity among QC samples. Reduced taxonomic bias improves the performance of biological assessments, facilitates transparency across studies, and refines estimates of diatom species distributions.