Coral reefs at Kaua‘i, O‘ahu, Moloka‘i, Maui, and Hawai‘i were surveyed using a rapid assessment method for marine nonindigenous and cryptogenic species commonly found in Hawaiian harbors and embayments with restricted circulation. In 41 sites surveyed by rapid assessment 26 nonindigenous and cryptogenic species (three algae, 19 invertebrates, and four fishes) were recorded from a total of 486 total taxa identified, and 17 of the nonindigenous and cryptogenic species occurred at only one or two sites. No more than six non-indigenous and cryptogenic species were recorded at any one site, and 21 of the 41 sites had fewer than three. By comparison, laboratory identification of samples collected from seven of the sites closest to harbors found 6–23 nonindigenous and cryptogenic species per site. Values for nonindigenous and cryptogenic species from rapid assessment were compared with factors potentially influencing spread and proliferation of introduced marine species. These factors included distances from harbors, boat-launching ramps, stream mouths, and shorelines; degree of shoreline urbanization; quantity of artificial surfaces in the water; reef condition and isolation from the open ocean; and native species richness. A best subsets regression model explained over 65% of the variance in nonindigenous and cryptogenic species from two predictor variables and their interaction: isolation from the open ocean and number of native taxa, with most of the variance explained by a highly significant relationship of nonindigenous and cryptogenic species with isolation from open-ocean conditions.