The complete genomic sequence of Pseudomonas syringae pathovar syringae B728a (Pss B728a), has been determined and is compared with that of Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). These two pathovars of this economically important species of plant pathogenic bacteria differ in host range and apparent patterns of interaction with plants, with Pss having a more pronounced epiphytic stage of growth and higher abiotic stress tolerance and Pst DC3000 having a more pronounced apoplastic growth habitat. The Pss B728a genome (6.1 megabases) contains a circular chromosome and no plasmid, whereas the Pst DC3000 genome is 6.5 mbp in size, composed of a circular chromosome and two plasmids. While a high degree of similarity exists between the two sequenced Pseudomonads, 976 protein-encoding genes are unique to Pss B728a when compared to Pst DC3000, including large genomic islands likely to contribute to virulence and host specificity. Over 375 repetitive extragenic palindromic sequences (REPs) unique to Pss B728a when compared to Pst DC3000 are widely distributed throughout the chromosome except in 14 genomic islands, which generally had lower GC content than the genome as a whole. Content of the genomic islands vary, with one containing a prophage and another the plasmid pKLC102 of P. aeruginosa PAO1. Among the 976 genes of Pss B728a with no counterpart in Pst DC3000 are those encoding for syringopeptin (SP), syringomycin (SR), indole acetic acid biosynthesis, arginine degradation, and production of ice nuclei. The genomic comparison suggests that several unique genes for Pss B728a such as ectoine synthase, DNA repair, and antibiotic production may contribute to epiphytic fitness and stress tolerance of this organism. Pseudomonas syringae, a member of the gamma subgroup of the Proteobacteria, is a widespread bacterial pathogen of many plant species. The species P. syringae is subdivided into approximately 50 pathovars based on pathogenicity and host range. P. syringae is capable of producing a variety of different symptoms depending on the host species and site of infection. For example, it causes leaf spot diseases that defoliate plants such as tomato, bean, soybean, trunk cankers, and so-called "blast" diseases on fruit, nut and ornamental species. Considerable variation occurs both between and within different pathovars of P. syringae (1). Because of its importance as a plant pathogen, it has been the subject of much research, especially of its epidemiology and virulence mechanisms (2). Pseudomonas syringae pv. syringae (Pss) strain B728a is typical of most strains of this pathovar in that it exhibits a very pronounced epiphytic phase on plants. Such strains achieve and maintain large populations on healthy plants, where they are exposed to stressful conditions such as dryness and sunlight that are hostile to bacterial growth(2). Epiphytic Pss populations serve as inocula that can subsequently invade plants and initiate disease. Pss strains are distinct from many P. syringae strains, such as P. syringae pv. tomato (Pst) strain DC3000, that poorly colonize the exterior of plants; these strains may be considered "endophytes" based on their ability to multiply mostly within the plant (3). True epiphytes such as Pss B728a often reach surface populations of over 107 cells/g while strains such as Pst DC3000 seldom exceed 105 cells/g (2, 3). Thus, these strains might be considered to occupy different ends of the epiphytic/endophytic spectrum of plant colonization as described by Beattie and Lindow (4). As a pathogen and an epiphyte, Pss B728a has evolved to exploit at least two distinct habitats: the leaf surface and apoplast. Because rapid changes in temperature, low water content, and incident solar radiation occur on leaf surfaces, it has been hypothesized that the epiphyte Pss B728a posseses more genes conferring environmental stress tolerance than the endophyte Pst DC3000 (4). Pss B728a also exhibits several traits such as ice nucleation activity and SR production (2) that are lacking in many other strains of P. syringae including Pst DC3000. As the most ice nucleation active bacterial species, P. syringae is responsible for inciting frost injury to frost sensitive plants that can supercool and avoid damaging ice formation if not colonized by ice nucleation active bacteria (2,4). We present here a genomic comparison between strains Pss B728a and Pst DC3000 of P. syringae pathovars as well as between these strains and P. aeruginosa and P. putida, two additional Pseudomonads recently sequenced. These genomic comparisons provide insights into the evolutionary history and diverse life styles of the pseudomonads, including their association with the environment, plant or mammalian hosts.