Quahog Parasite Unknown (QPX) is a potentially lethal pathogen of the hard clam Mercenaria mercenaria along the northeastern coast of the United States. To enumerate QPX in clams and in environmental samples, a SYBR Green real-time quantitative PCR (qPCR) assay targeting the ITS region of the QPX rRNA operon was developed. The qPCR assay was used to test samples collected in 2006 from the site of a recent QPX disease outbreak in Raritan Bay, NY, and from a site where QPX has not been detected in Peconic estuary, NY. No QPX was detected in any seawater sample analyzed while QPX was detected at abundance between 34 and 215 cells mg<super>-1</super> in four sediment samples. At the three Raritan Bay sites studied in 2006, QPX prevalence and infection intensity in clams examined by both histological and qPCR assays showed a temporal pattern, suggesting a relationship between QPX infection and temperature. Laboratory-based experiments were conducted to study the effect of temperature on parasite abundance and mortality in experimentally and naturally infected clams. Clams kept at 13 øC always showed higher mortality as well as higher QPX prevalence and weighted prevalence compared to those at 21 and 27 øC after 2 or 4 months incubation, suggesting that under lab conditions, low temperature could be more advantageous for QPX than clams in the host-pathogen interaction. The transmission experiments conducted in this study also revealed that low temperature may promote QPX transmission between cohabitated infected clams and susceptible clams. At 13 øC, some susceptible clams acquired QPX cells at rare to moderate levels of abundance after 2 to 3 month cohabitation with naturally infected clams, while no QPX was detected by qPCR in susceptible clams after being co-incubated with naturally infected clams at 21øC. The labyrinthulomycetes, the larger phylogenetic group to which QPX belongs, are a group of ubiquitous but rather poorly understood marine protists. 18S rRNA gene-based qPCR assay and terminal restriction fragment length polymorphism (T-RFLP) analysis were developed to assess the abundance and diversity of labyrinthulomycetes in sediment and seawater samples collected from Raritan and Peconic Bays in 2006. T-RFLP analysis revealed temporal changes in labyrinthulomycete community structure in both sediment and seawater samples, although the pattern was more distinct in seawater. The composition of labyrinthulomycete communities in sediment was significantly different from those in seawater samples. Labyrinthulomycete community structure was not related to the prevalence of QPX disease in clams collected along with the sediment and seawater samples.