The marine and estuarine invertebrate and fish communities in Pearl Harbor, Oahu, Hawaii were surveyed between January and October, 1996. Samples were taken and observations were made at fifteen stations throughout the harbor, in a variety of environments ranging from near oceanic conditions at the harbor entrance channel to areas receiving land runoff with high sediment loads and turbidity. All organisms were identified to species or the highest practicable taxonomic level, and results were compared to previous published and unpublished marine biological surveys conducted in the harbor, published taxonomic descriptions of organisms collected from the harbor and Pearl Harbor specimens cataloged in the Bernice P. Bishop Museum collections. All data were entered on a relational database at the Bishop Museum (database is not included in this dataset) which enables tracking the appearance of individual species with time. Based on a number of criteria, nonindigenous and cryptogenic (i. e. origin unsure, but with good evidence of being introduced) species were designated and their introductions noted on a timeline beginning from the first organisms reported in Pearl Harbor in the last century. This study collected or observed a total of 434 species or higher taxa (36 algae, 1 spermatophyte, 338 invertebrate and 59 fish) from the 15 stations sampled, the highest number of taxa that have been collected for any Pearl Harbor study. Ninety six species, or about 22%, are considered to be introduced or cryptogenic. The areas of highest species richness were in the entrance channel and in Rainbow Bay at the northeast head of East Loch where number of taxa were around 150. Lowest species richness occurred in the areas of high sedimentation and turbidity at the head of West Loch where fewer than 50 taxa occurred. Dendrographs based on Sorensen Indices of Similarity of species composition among stations suggest three types of communities in the harbor, one associated with relatively oceanic conditions in channel areas, one with the highly turbid West Loch sedimentary environment and one with conditions prevailing throughout the rest of the harbor. This report also contains historical maps, a chronology of important events, and a bibliography of related work.