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In this study, in order to assess the ecological health status and zoning of soft bottom of Gorgan Bay, the spatial and temporal distribution of macrofauna and their relationship with environmental stress were investigated. Sediment samples were collected using a Van Veen grab at 22 sampling points, seasonally during 2012-2013. The averages (±SD) of the percentages of sand, silt, clay and TOM (Total Organic Matter) in the sediment samples were determined (44.4± 15, 53.4 ± 14, and 2.2 ±2.2 and 7.2% ± 1.6, respectively). Our results showed that mean (range) of Al, As, Cu, Fe, Ni, Pb and Zn in the sediment samples were 1.2 % (0.4-2.1), 4.8 (2.5- 10.3) ppm, 10.5 (4.4-16.9) ppm, 1 (0.4 – 1.6) % , 13.6 (6.2-21.5) ppm, 9.1 (4.7-12.9) ppm and 23.9 (3.1-39.4) ppm, respectively. In spring, both Al and Ni were higher than the guideline level. In the event that arsenic was exceeds the guidelines in summer. In this study, 14 species of macrofauna from 12 families were identified. Polychaeta with 3 species was the most dominant group in terms of abundance. The four most abundant taxa making up 85% of all specimens (Streblospio gynobranchiata, Tubificidae, Hediste versicolor and Abra segmentum). The western area were characterized by the higher species diversity (H', 1.94). So Gorgan Bay presents transitional macrobenthic assemblages that are spatially distributed along substrate gradients .The mean of Shannon index, BENTIX, BO2A, AMBI and M-AMBI in the bay was 1.3, 2.2, 0.4, 3.2 and 0.65 respectively. According to the results of these indices, ecological status of the western part of the bay assessed better than the other parts. According to the results of the nmMDS (non-metric Multidimensional Scaling), PCA (Principal Components Analysis), the map of distribution of heavy metals and the map of the ecological status , it seems Gorgan Bay is divided into two separate zones (the eastern and the western parts).M-AMBI finaly introduced reliable index for assessing the ecological status of the Bay.