Aims: Effects of amino acid on morphological development and nucleus formation of arachidonic acid-producing filamentous micro-organism, Mortierella alpina were investigated using flow-through chamber. Methods and Results: Mortierella alpina CBS 754.68 was cultivated in flow through chamber using nutrient-rich, minimal and specific amino acid-containing minimal media. To investigate the effect of amino acid on morphological parameters either 0.28 g l(-1) alanine, 0.53 g l(-1) sodium glutamate one hydrate or 0.42 g l(-1) valine was added to the minimal medium. In a flow-through chamber, the growth of hyphal elements and nucleus formation of arachidonic acid-producing fungus M. alpina were studied on-line, using image analysis techniques. When the Ala- and Val-containing media were used, the hyphal growth units (HGUs) were 90.2 and 86.7 mu m per tip, respectively, which were 2.4-fold higher than that in the nutrient-rich medium, indicating that Ala and Val stimulate the elongation of hyphae. The specific nucleus formation rates were Glu-> Val-containing media > minimal and nutrient-rich media > Ala-containing medium. The nucleus doubling times in Glu- and Val-containing media were 1.9 and 2 h, respectively, which were not significant different. Conclusions: Ala and Val stimulate the elongation of M. alpina hyphae, and nucleus formation rates were Glu-> Val-> Ala-containing media. Significance and Impact of the Study: Formation of fungal morphology and nucleus were shown using the flow-through chamber coupled with image analysis, which making possible to discuss the relationship between mycelial morphology and nucleus formation of M. alpina.