Magnetic separation with composite microspheres presents an alternative strategy for applications in biomedical and bioengineering fields. However, the synthesis of core–shell structured magnetic composites universally assumes the surfactant-directing and/or silica-assisting polymerization approach to modify and stabilize the magnetic cores. In this paper, we report on the surfactant-free synthesis of well-defined core–shell structured Fe₃O₄@PANI and Fe₃O₄@PPy microspheres with high magnetization. The temperature dependence of magnetization of the samples was examined as a function of temperature between 3 and 300 K in an applied field of 500 Oe. It was found that the blocking temperature (T_B) values of the composite spheres are well above the room temperature. The small variation in magnetization as the temperature changes renders the composite spheres a suitable candidate when used at elevated temperatures. Also, the genomic DNA can be effectively isolated from Aspergillus niger (A. niger) cells with the composite microspheres, using a PEG–NaCl binding buffer and a phosphate eluting buffer. The magnetic isolation of genomic DNA with the composite microspheres was shown to be superior to the conventional phenol–chloroform extraction, which was confirmed by agarose gel eletrophoresis and polymerase chain reaction (PCR) diagnosis. The Fe₃O₄@PANI and Fe₃O₄@PPy microspheres presented here have great potential in enzyme immobilization, drug delivery, catalysis, and sensors.