The results of the studies on the influence of various protection systems on the phytosanitary situation in planting colored potato varieties in the conditions of the Novosibirsk region are presented. It has been established that the chemical protectant Celest Top more effectively reduces the development of rhizoctoniosis (black scab) in comparison with the biological preparation Bactofort. On average, this indicator when using the chemical system was significantly lower by 4.8 times in the germination phase, and 2.0 times lower in the period of budding-beginning of flowering of the culture. A significant influence of the optimization of mineral nutrition for the biological preparation Bactofort was established, in this case, against the background of mineral fertilizers, the development of rhizoctoniosis is 1.2 times lower. In the phase of budding – the beginning of flowering the disease development on the fertilized background with the use of chemical system of protection is marked significantly higher by 1.4 times in comparison with the background of natural fertility, with the biological system in this period this indicator has no differences. The number of the Colorado potato beetle when using the chemical system was significantly lower by 3.6 times in comparison with the biologized one. Optimization of mineral nutrition with the use of a chemical protection system significantly increased the number of the pest by 5.0 times in comparison with the background of natural fertility, while with a biological system this indicator does not have significant differences. The productivity of the culture is significantly higher when using a chemical protection system in comparison with a biologized one by 1.5 times. On a fertilized background, when using a chemical protection system, the productivity of potatoes is significantly higher by 1.2 times in comparison with the background of natural fertiity. At the same time, with a biologized system, this indicator does not have significant differences. Individual reaction of the varieties to the studied protective techniques has been noted. Among the four varieties studied, All Red should be singled out, in which the development of rhizoctoniosis on the stems on both protection systems at both levels of mineral nutrition was generally the smallest among all variety samples. The varieties All Red and Violet were the least populated by the Colorado potato beetle – an average of 0.50–0.55 ind./plant. The highest yield was obtained when growing the Rosemaria variety (average factor 22.3 t/ha). To control rhizoctoniosis and Colorado potato beetle on potatoes, it is possible to use biological protection systems, but taking into account the biological characteristics of the varieties.