||一、 There were two fishing types in this fishery. A lower number hooks of per basket (8-11 hooks), was operated majorly in the higher latitude of waters (north of 15oN and south of 15oS) to target on albacore; and other is using higher number hooks per basket (15-18 hooks), was operated majorly in the lower latitude of waters (15oN-15oS) to target on bigeye tuna and yellowfin tuna. The standardized catch per unit effort (CPUE) of Atlantic bigeye tuna and yellowfin tuna caught by Taiwanese longline fishery was estimated by general linear models (GLM). For the manipulation, several factors were possibly used including year, quarter, subarea, vessel category and the two-way interactions. Before estimating CPUE, model selection was done by stepwise regression, also historical catch and effort data were selected and re-examined by spatial and temporal distribution in the tropical core fishing area; then the 1981-2012 catch and effort data within the tropical core area (15oN – 20oS) were selected as tropical area and other the temperate area, and stratified into 5 subareas for each area to make the nominal CPUE homogeneous as possible among subareas by cluster analysis. The GLM and Delta-GLM were used to standardize boyh tropical tunas’ CPUE for Taiwanese longline fishery in the Atlantic tropical waters. The results obtained are very similar trend in comparison with before estimated,but the displacement of peaks in the series; and discrepancies have occurred with Japanese longline CPUE series. Logically, the comparison suggests that the applicability of Standardized CPUE for bigeye and yellowfin tuna by Taiwanese longline fishery in the Atlantic Ocean wants verification and refinery before stock assessment session. For Pacific Bluefin tuna, the standardized catch per unit effort showed a significant declining trend from 1999 to 2002, restored and stayed steadily in 2003 and 2004; dropped again in 2005 and remained with a slight fluctuation until 2008, then decreased to the historical lowest level of this series in 2010, then increased. As the result, the unloading port significantly transferred indicates that the unloading port may be an important factor during abundance index standardization.