Feces of harbor seals (Phoca vitulina richardsi) and hybrid Glaucous-winged/Western gulls (Larus glaucescens/occidentalis) from Washington State's inland marine waters were examined for Giardia spp. and Cryptosporidium spp. to determine whether genotypes carried by these wildlife species were the same as those that commonly infect humans and domestic animals. Using immunomagnetic separation followed by direct fluorescent antibody detection, Giardia spp. cysts were detected in 42% (41/97) of seal fecal samples. Giardia spp.-positive samples came from 90% (9/10) of the sites, and the prevalence of positive seal fecal samples differed significantly among study sites. Fecal samples collected from seal haulout sites with > 400 animals were 4.7 times more likely to have Giardia spp. cysts than were samples collected at smaller haulout sites. In gulls, a single Giardia sp. cyst was detected in 4% (3/78) of fecal samples. Cryptosporidium spp. oocysts were not detected in any of the seals or gulls tested. Sequence analysis of a 398 base pair (bp) segment of Giardia duodenalis DNA at the glutamate dehydrogenase (GDH) locus suggested that 11 isolates originating from seals throughout the region were a novel genotype and 3 isolates obtained from a single site in south Puget Sound were the G. duodenalis canine genotype D. Real-time TaqMan polymerase chain reaction (PCR) amplification and subsequent sequencing of a 52 bp small subunit ribosomal DNA region from novel harbor seal genotype isolates showed sequence homology to canine genotypes C and D. Sequence analysis of the 52 bp small subunit ribosomal DNA products from the 3 canine genotype isolates from seals produced mixed sequences that could not be evaluated.