This study was aimed to study the effect of physicochemical parameters on Aspergillus niger HFD5A-1 growth and pectinase production. The newly isolated fungal strain, Aspergillus niger HFD5A-1 was cultivated in 250 ml Erlenmeyer flask under submerged fermentation and physicochemical characteristics were studied in order to enhance the pectinase production. Fermentation conditions improved were pH 4.5, cultivation temperature of 30°C, inoculums size of 2% (v/v) 1 × 10⁶ cell/mL and agitation speeds of 150 rpm, together with citrus pectin of 1.80% (w/v) and 0.40% (w/v) of peptone as carbon and nitrogen sources, respectively had produced the highest pectinase production of about 2.51 U/mL and 6.58 g/L fungal growth after 6 days of incubation time. The results show that after improvement of physicochemical parameter the pectinase production was increased about 97.6%. The enzyme production by this isolate was found that not growth dependent. Improvement of physicochemical parameters is an important factor in pectinase production in submerged fermentation system.