The seasonal variability of free and protein bound amino acids (AAs) in the sediments of mangrove ecosystem, west coast of India were studied. AAs exhibited significant variability with depths in the sediments of two mangrove ecosystems, Mangalavanam and Vypeen, situated on the west coast of India. Of the ten AAs detected, serine (Ser) was the most abundant followed by threonine (Thr), glycine (Gly), aspartic acid (Asp), tyrosine (Tyr), glutamic acid (Glu) and alanine (Ala). The trend in AA relative abundance in the sediment and leaves exhibits a close similarity indicating a major influence of plants in the supply of these compounds to the sediment. The most common AAs at both stations are Asp, which is abundant in sediments with a large organic inputs followed by Glu, which is abundant in phytoplankton and marine bacteria. Ser, Thr and Gly, which constitute diatom cell walls, were also found in significant concentration. The changes in relative abundance of various AAs with depth indicate significant seasonal variability. This may be due to the selective microbial utilization of these AAs at different depths. Principal component analysis (PCA) revealed that the first principal component, which is the degradative index (PC I ) has ca . 84 % of the variance at Mangalavanam and