The study conducted to evaluate of two common disinfectant, Methylene blue and Chloramine T, on bacterial and fungal loads of Koi carp juveniles. Experimental treatments performed in a complete randomized design.210 koi carp juvenile by average weight of 1.5 g stocked in 20 l plastic tanks. Treatment dosage were including control, three dosage of methylene blue (2, 3 and 4 ppm) three dosage of chloramine T (10, 15 and 20ppm) each dosage considered with three replicates. Fish disinfection done during a three days period as 30 min. bath. At the end of third day microbial and fungal culture and has done as superficial culture of gill and skin. Statistical assay results showed that using 20ppm of chloramine T and 4 ppm of methylene blue comparing controls and other treatments had significant decreasing effects on bacterial and fungal flora of sampled organs (P<0.05).