PURPOSE:To obtain a microorganism controlling agent having long-term storage stability, capable of also standing long-term use and having improved stability. CONSTITUTION:The objective microorganism controlling agent contains (A) one or more kinds of isothiazolone compounds expressed by the formula (R is H, alkyl, lower alkenyl, lower alkynyl or benzyl; X and X' are H or halogen; M is cation of ammonium, alkaline earth metal or heavy metal; Z is anion capable of forming a compound with M having solubility enough to water; (a) is 1 or 2; n is integer wherein Z can satisfy valence of M), especially 5- chloro-2-methyl-3-isothiazolone magnesium chloride, (B) 2-bromo-2- nitropropane-1,3-diol and (C) gluconic acid or salt thereof and has safety. In the controlling agent, the interior of circulating water system such as water system for heat exchange in temperature controlling equipments of industrial product-producing process or building, etc., is prevented from the breeding of bacteria, algae, etc., and storage stability for suppressing formation of slime is improved.