Abstract: The characteristics and sources of fluorescent dissolved organic matter (FDOM) in the ship ballast water of forty-two inbound ships docked at Yangshan Port and Jiangyin Port were determined by three-dimensional excitation−emission matrix spectroscopy (3D-EEMs) combined with parallel factor analysis (PARAFAC). The difference in FDOM between the exchanged and unexchanged ship ballast water samples was also evaluated based on the analysis of fluorescent components. The results indicated that the FDOM of ships' ballast water was mainly composed of three fluorescent components: one tryptophan-like component C1 (275/332 nm), UVB humic-like component C2 (290, 315/386 nm) and UVA humic-like component C3 (250, 360/446 nm). The tryptophan-like component C1 had the highest percentage of fluorescence intensity in ship ballast water, followed by the UVA humic-like component C3, and the humic-like component C2 had the lowest proportion. The fluorescent component C1 in unexchanged ballast water was significantly higher than that in exchanged ballast water (p＜0.05), while there was no significant difference in component C2 or C3 between the unexchanged and exchanged ballast water (p＞0.05). Fluorescence index analysis showed that FDOM in the unexchanged ballast water was affected by the combined effects of terrestrial input and biological activities. Biological activities constituted the main source of FDOM in the exchanged ballast water since it was away from near shore. There was a significant correlation between UVB humic-like component C2 and UVA humic-like component C3 in unexchanged samples (p＜0.01), while significant correlation was found for the three fluorescent components in exchanged ballast water (p＜0.01). It could also indicate that there were differences in the origin of FDOM in the two types of ballast water. Principal component analysis showed that there were more significant differences between exchanged or unexchanged ballast water, using the fluorescence intensity, fluorescence index (FI) and salinity. Afterwards, the characteristics and source of ballast water can be analyzed more accurately in combination with other factors such as physico-chemical properties and holding time.