Studies on chromosome manipulation of domestic species such as small abalone, oyster, carp and loach have been conducted by physical or chemical methods in Taiwan. It was emphasized in this study how to avoid the complicated procedures and fluctuated results by using the automatic device and optimal protocols with the step-wisely improved outcome in terms of accuracy and reproducibility. Time-dependent development of newly fertilized eggs in experimental target fish, cyprid loach, was observed to understand range of possible timing to retain their polar bodies at ambient temperature. Maturation induction of female spawners was usually done and a large amount of eggs at the same stage was obtained. Applications of physical or chemical treatments in manual or automation methods on newly fertilized eggs in loach were found to result in feasible chromosome manipulation with the favorable order of cold shock, chemical shock and heat shock. DNA contents in blood or ground fin in cell suspension were investigated by flow cytometer and were found suitable to identify the presence of triploid individuals.After proper improvement of hardware in the automation system by being equipped with a big low temperature circulator early in this year, it ensured the adequate supply of water for cold shock at favorable temperature such as 1 to 3 ℃. A total of 28 chromosome manipulation trials were done. Considering the integrated index of fertilization rate and hatching rate of loach eggs, it was found that in 3 ℃ treated groups was always at least two times higher than that in 1 ℃ group no matter in case of cold shock starting at 7mpf and lasting for 20, 30, or 40 min and in case of cold shock starting at 4, 7, 10mpf and lasting for 20 min. In all well manipulated and smoothly grown-up groups of G, I, J, K, L,S, U, X, Y, and Z, there was the presence of triploidy. The obvious subgroups with favorable DNA content against that of its corresponding control were 2008-L3 (154.94：100.65)；2008-J1、J2、J3 (153.50：99.65、145.98：99.50、144.77：100.41)；and 2008-X1、X2、X3 (154.69：99.65、145.98：99.50、144.77：100.41)。 It was proved that stepwise improvement of hardware and software resulted in the expected and repetitive positive results.Therefore, technologies of chromosome manipulation in automation system originally designed only for shellfish have now become available for fish species after optimization of species-specific parameters. The prospects is that researchers and aquaculturists will adopt scientific manipulation technology to produce polyploidy in fish and shellfish because of the accessibility of the multifunctional automation system with the advantages such as saving energy, saving time, avoiding man-made mistakes, and promoting the replication of anticipated results. In total, this paper summarizes the related strategies to obtain encouraging results and experience to aspire progress in the development of automation system of chromosome manipulation for fish. It is expected that the automation system thus developed will play a role in mass-scale chromosome manipulation that are not related with gene modification and thus accepted by the global market in fishes and shellfishes.