SUMMARY.1. A taxonomic analysis of 171 phytoplankton samples obtained from Crater Luke, Oregon, between 1985 and 1987 revealed 132 taxa in the upper 250 m of the water column. The greatest temporal variation in taxonomic structure occurred between 40 and 80 m below the water surface, a depth range which corresponded to the zone of maximum primary production.2. Phytoplankton cell biovolume in the upper 20 m of the water column was relatively high during the summer months, a period whenNitzschia graciliswas dominant in the epilimnion. However, 72% or more of the cell biovolume between 0 and 200 m was distributed below 20 m and, during the winter and spring months, 61% was found below 80 m.3. Cluster analysis identified a sparse, temporally ubiquitous flora which was modified to various degrees when environmental conditions became favourable for the growth of a few dominant taxa. These surges ot dominance by individual taxa accounted for 2 to 5‐fold increases in cell biovolume and generated a pronounced taxonomic discontinuity between the floras in the epilimnion and hypolimnion.4. While the taxonomic structure of the phytoplankton in the epilimnion corresponded closely with the structure found in a 1978–80 study, the flora below the metalimnion was more diverse and less predictable in species composition than the pattern reported in the earlier st