PKMiner is a web-based system to provide comprehensive collection of bacterial aromatic polyketide and thier biosynthetic proteins called Type II polyketide synthases (PKSs) and a systematic framework for the analysis of protein or genome sequences. Currently, PKMiner contains 42 known bacterial aromatic polyketide together with 280 type II PKSs from the report in literature and 40 type II PKS gene clusters including 231 predicted type II PKSs obtained from the analysis of currently available 319 actinobacterial genomes. The type II PKSs were identified using type II PKS domain specific classifiers and their gene clusters were further analyzed for the identification of aromatic polyketide chemotypes based on the prediction rules generated by the combination of known type II PKS domains. PKMiner includes interactive analysis and navigation tools that make it possible to identify novel type II PKSs and analyze their type II PKS gene clusters with graphical illustration and summarized description.