In Taiwan, the recruitment season for Anguilla marmorata glass eels is usually between March and October, with two peaks usually occurring in spring and autumn. In this study, we aimed to compare potential differences in the growth of spring and autumn A. marmorata glass eels, which could be used as a selection index for aquaculture by eel farmers in Taiwan. The spring A. marmorata glass eels were collected in June 2018 and March 2019, while the autumn glass eels were collected in December 2018 and September 2019. The glass eels were reared in three tanks (40 fish per tank; 28 ± 1 °C) equipped with nitrification filters and were fed commercial frozen red worms (Chironomus dorsalis) twice a day and six days a week. The total length (TL) and body weight (BW) of the eels were measured every two weeks. The results showed that the final mean TL and BW were 68.3 ± 3.9 mm and 0.46 ± 0.12 g, respectively, for the spring group, and 73.1 ± 5.3 mm and 0.58 ± 0.14 g, respectively, for the autumn group. No significant differences in the mean TL were detected between these two groups in any week (p > 0.05). The mean BW of the spring group was significantly higher than that of the autumn group in week 4 (p < 0.05). No significant differences in percentage weight gain and condition factor were observed between the two groups (p > 0.05). This result suggested that, although the spring and autumn groups may be from different stocks with different spawning times and geographic regions, the initial growth potential of the two groups was not significantly different. Thus, the findings of this study demonstrate that both spring and autumn recruits of glass eels fit the aquaculture needs.