Extraction of high molecular weight genomic DNA (HMW-gDNA) from spider organs and construction of an electroelution system for obtaining HMW-gDNA efficiently are described. We improved the CTAB method to isolate genomic DNA from spider pectoral muscle tissues, constructed a novel electroelution system with the use of 2-mL centrifuge tube and dialysis membrane, and utilized this self-constructed electroelution system to recover target HMW-gDNA from agarose gels. The HMW-gDNA extracted using the improved CTAB method could be over 48.5 kb in size. By trapping the HMW-gDNA with dialysis membrane, the electroelution system could recover target HMW-gDNA from agarose gels rapidly and without affecting the integrity of HMW-gDNA. The recovery rate was over 75% with the OD260/OD280 ranging from 1.8 to 2.0. The results demonstrate that the improved CTAB method can be used to extract spider HMW-gDNA, and the electroelution system is a general method for recovering target HMW-gDNA from agarose gels with low cost, simplicity, high efficiency and good practicability.