A new record of pineapple disease in Taiwan was investigated. The disease did not cause apparent symptoms on pineapple plants or fruit surfaces, but it induced browning and mild soft-rot to the fruit flesh, similar to the pineapple marbling disease caused by Pantoea ananatis. Based on the symptom and pathological studies, physiological and biochemical analyses, Biolog GN2 and MIDI Sherlock Microbial Identification comparisons, the pathogen was identified as Burkholderia gladioli. PCR identification showed that the pathogen, same with B. gladioli isolated from various host plants, contained a DNA segment of 388 bp that is not found in P. ananatis. Results from 16S rDNA sequencing and comparison revealed that the degree of similarity to the ones of B. gladioli reached 99%. Besides, eleven commercial agrochemicals were tested and all found to inhibit the growth of this pathogen; among which, oxolinic acid was identified to be the most effective one.