The invention provides a reagent kit which extracts zooxanthella genome DNA from reef building coral and a method of the reagent kit. The reagent kit comprises: reagent A (lysis buffer), reagent B (protease E), reagent C (RNAase A), reagent D (supersaturation NaC1 solution), reagent E (DNA cleaning mixture) and reagent F (DNA eluent). The method of the invention comprises: firstly, using the lysis buffer which contains SDS to crack tissue cells, then, providing a high salt low PH circumstance, enabling protein in solution to degenerate further, but combining DNA on a silica gel column, and finally, quantitatively reclaiming the DNA from a chromatography column in water-soluble buffer solution. The zooxanthella genome DNA can be rapidly and conveniently extracted from varous reef building coral, the DNA which is obtained can be used to research molecular ecology, systematic evolution and the like, and thereby the demands of regular monitoring tasks in coral reef nature reserves can be satisfied.