The community structure and catabolic functional diversity of indigenous rhizosphere fluorescent pseudomonad isolates recovered from un-amended soil (control treated) and following long-term (6 years) swine compost application (compost treated) were studied. Soils collected for the pot experiments were from a Taiwanese experimental farm established in 1995 to study the long-term effects of crop rotation and organic amendment. In the pot experiments, corn seed was cultured; after the elongation stage, 13 and 32 indigenous rhizosphere fluorescent pseudomonad isolates were collected from compost-treated (n=13) and control-treated (n=32) soils. All isolates were classified by 16S rDNA restriction fragment length polymorphism (RFLP) and unweighted pair-group method using arithmetic averages analyses. Most (84.4%) of the control-treated soil isolates belonged to genotype A, which corresponded to Pseudomonas putida based on 16S rDNA sequences analysis. However, only 61.5% of compost-treated soil isolates were from genotype A; 30.7% of the isolates belonged to genotype B, whose 16S rDNA profile corresponded to Stenotrophomonas maltophilia. Differing catabolic potentials of the P. putida isolates from control- and compost-treated soils were evident; isolates from control-treated soils utilized organic acids including citric acid, cis-aconitic acid, and formic acid more actively than compost-treated soil isolates. Moreover, the latter isolates more efficiently utilized carbohydrates of i-erythritol and l-rhamnose than P. putida isolates from control-treated soil, consistent with the alteration in the catabolic functions of indigenous rhizosphere P. putida by long-term compost application.