On the base of monitoring of water quality for aquaculture, performed since 2010, it is noticed that two positions are showing increased level of trophicity and bacteriological contamination. Changes in sanitary quality of farms are especially intensive during the summer months, so the results of basic physical, chamical and biological parameters, measured during periods June-September 2010 and 2011 are presented and compared.

This paper presents results of measuring the contents of certain bioindicators in samples of digestive gland and lung of mussels (Mytilus galloprovincialis). The results were obtained in the framework of the Program for monitoring ecological status in Montenegro from 2009 to 2011 year. Samples were collected from two locations: Kotor-Dobrota (wild mussels) and the site of Bijela (caged mussels). Dynamic of sampling was twice a year, in April and September. In order to estimate the spatial distribution and temporal trends of pollution the results were compared with analysis of biomarkers in the three localities in the Slovenian coastal waters (bays Piran, Koper and Strujan). Biomarker responses showed no differences between these positions in the southern and northern Adriatic.

Monitoring of ecological condition of the coastal sea of Montenegro has been carried out extensively since 1963 along with foundation of the Institute of marine Biology in Kotor (Montenegro). Recently, in accordance with recommendations of the Barcelona Convention, the LBS Protocol, the EU Framework Directive for coastal waters and domestic laws, in recent years has been carried out continuous monitoring of quality water, sediments, biota as well as ecological effects of pollution on constant monitoring positions in this southeastern part of the Adriatic. In this paper was given an over view of activities and the plan of long-term continuous monitoring of environmental quality and ecological condition of the coastal sea of Montenegro.

Qualitative and quantitative phytoplankton analysis was determined using standard microscopic methods and high performance liquid chromatography (HPLC) in the Bay of Kotor, seasonally, from April 2008 to March 2009. Diatoms represents dominant group of microphytoplankton with maximum in spring period. Dinoflagellates reached maximum value in summer period, and followed by cyanobacteria bloom. Dominant biomarkers, fucoxanthin, alloxanthin, 19'-heksanoloksifukoxanthin, zeaxanthin and chlorophyll b, show a similar distribution as the appropriate phytoplankton assemblages during the researches in Kotor Bay.

New locations for the distribution of algae C. corniculata (Phaeophyceae) are presented, with a scope to improve scarce knowledge on phytobenthos of the Montenegrian coast. In the Bay of Boka Kotorska this algae is found on 10 locations and on 3 locations, on depth of 3 m and 5 m, measurements of wet weight and length of primary branches are done. Differences between biomass of algae are note between different depths and different seasons, but between different locations there are no significant differences.

In the beginning of 2008, on the Montenegrin coast is confirmed finding of new species, what was unknown until now in this part of Adriatic sea. The Sphoeroides cutaneus is tropical species with habitat in warm sea around Japan, China and Indonesia. Probably is one of the Lessepsian migrant. It tooks around 130 years for a fish to come through Suez Canal and Red Sea to Mediterranean, then through Otrant Strait into Adriatic sea. It is possible, also that this apparition has something with the global climate change and temperature rise in saltwater in Mediterranean as well as in Adriatic.

During the first five months of 2007 at one station in front of the entrace the Bay of Boka Kotorska, it was collected mesozooplankton using Nansen net, mesh netting of 200 microns. Analyses included determination of biomass and qualitative composition. Data are given on the number of specimens per cubic meter as well as on the volume organisms. Qualitative composition showed domination Copepoda of zooplankton groups.

Mediterranean mussels, Mytilus galloprovincialis, are recognized bioindicators used in investigation of genotoxic pollution in the areas under the impact of anthropogenic activities. In July and August 2011 specimens of M. galloprovincialis were collected from 5 sites of Boka Kotorska Bay, Montenegro. Level of DNA damage was measured in gills, haemolymph and digestive gland with alkaline comet assay. Significant increase in DNA damage was detected in tissues of mussels collected from polluted sites comparing with mussels collected from the clean reference site Dobrota. The highest response to pollution was found in gills and digestive gland cells.

Based on all available data a review of introduced non-indigenous species is reported for the area of Montenegrian coastal sea (South-East Adriatic Sea). All together 11 species were recorded, three algae and eight animals. Monitoring of invasive species has been done partially only for Caulerpa racemose var. cylindracea, while for other species distribution and impact on autochthonous environment is unknown.

During the continuous analysis of zooplankton and hydrographic quality of sea in Boka Kotorska bay in season series during 2007/08, in addition to the other zooplanktons groups, fauna was analyzed, the appearance and abundance of Siphonophorae. Special attention was applied to biodiversity, dynamic abundance and distribution of group. In this paper we are exposing the data for abundance and distribution of group of Siphonophorae from Boka Kotorska Bay. We have found six species of which only the species Muggiaea cochi (W and l l) can be located throughout the year at all stations and in shallow stations only in summer. The other species Lensia conoidea (Keferstein et Ehlers), Lensia multicristata (Moser), Lensia subtilis (Chun), Lensia fowleri (Bigelow), Abylopsis tetragona (Otto) occur rarely in small numbers or in individual specimens.