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SUMMARY In Lithuania fifteen plant species included into Annex II of the Habitat Directive were recorded. Twelve of these species are vascular plants (Agrimonia pilosa, Aldrovanda vesiculosa, Botrychium simplex, Caldesia parnassifolia, Cypripedium calceolus, Dianthus arenarius subsp. arenarius, Linaria loeselii, Liparis loeselii, Najas flexilis, Pulsatilla patens, Saxifraga hirculus, Thesium ebracteatum), whereas other 3 are bryophytes (Buxbaumia viridis, Dicranum viride, Hamatocaulis vernicosus). Results of investigations on population structure and habitat state of 12 plant species (Aldrovanda vesiculosa, Agrimonia pilosa, Botrychium simplex, Cypripedium calceolus, Dianthus arenarius subsp. arenarius, Linaria loeselii, Liparis loeselii, Najas flexilis, Pulsatilla patens, Saxifraga hirculus, Thesium ebracteatum and Hamatocaulis vernicosus) performed in the year of 2015 are presented in this report. In total, 103 populations of plant species, occurring in 65 territories (55 in important habitat areas and 8 outside of the protected areas) were evaluated. Methods for monitoring of populations and habitats of protected species which were started to investigate in previous years were corrected and supplemented and methods for two water plant species (Aldrovanda vesiculosa, Najas flexilis) were created and tested. Populations of each investigated species were described as well as location of populations; state of their habitats, implemented management measures and other important information is provided. Plant communities in which populations of protected species were described and changes which took place in the communities were analysed. Parameters of morphological measurements were analysed and compared with the results of previous investigations. At the end of analysis of data on each species, conclusions and necessary measures for species conservation are provided. Populations of have Agrimonia pilosa changed differently. In one population the number of individuals significantly decreased, whereas in other population – increased. State of the population in Naudvaris forest has improved because management measures according to individual management plan were implemented. Population of is abundant Aldrovanda vesiculosa and favourable. The improvement of the habitat and population state took place because of implementation of conservation measures in the years of 2013 and 2015. Single registered population of Botrychium simplex in Lithuania, which is situated in is still unrecovered and the state of this species population in the country remains unsatisfactory. Thorough investigation on potential habitats of this species is required as well as more intense management of the habitat in Žemaitija National Park. In populations of Cypripedium calceolus the decrease of the number of individuals is observed because of plants flower poorly and fruit-set is very low. Therefore the renewal of populations is very slow or absent. The greatest threat for populations of this species rise from unfavourable conditions of habitats related to an inappropriate forest management practice. The single known population of Dianthus arenarius subsp. arenarius has increased in the number of individuals because the habitat was managed. The damage of moss cover created favourable conditions for germination of seeds. The increment of young individuals in the population is the indicator of plant recruitment. Population of Linaria loeselii situated in strict reserve zone was found to be more numerous to compare with previous years, whereas populations situated in recreational zones have decreased significantly or became extinct. This species is also threatened by the invasion of alien species. Only small portion of Liparis loeselii populations are viable and abundant. Many of populations are small and their demographic structure is unfavourable for long-term stability. The main threat for this species is succession changes of habitat conditions. It is necessary to prepare conservation plan as well as population management plans for this species and to implement them immediately. Urgent correction of nature management plans is required as inappropriate measures are proposed for conservation of this species. The population of Najas flexilis is critically endangered in single known locality in Lithuania. During investigation only one individual of this species was recorded. It is necessary to prepare species conservation plan and to implement it immediately. State of most of Pulsatilla patens populations is unfavourable for their survival because of inappropriate habitat conditions. Populations of this species occurring in habitats managed in the years of 2013 and 2014 according to species management plan significantly increased both in the total number and the number of generative of individuals. Several populations of this species in protected areas are in critical condition or are supposedly extinct. The main part of Saxifraga hirculus populations are in critical state because their habitats are significantly degraded. State of three populations in which habitats conservation measures have been implemented in the years of 2013 and 2014 improved significantly. Artificial propagation of plants proved to be very effective measure of conservation. Most of habitats of Thesium ebracteatum are small and this species is threatened by unfavourable changes of their habitats, as meadows and forest edges overgrow by shrubs and trees. This species is also threatened by invasion of alien plant species. It is necessary to prepare and implement conservation and management plans for tjis species. The state of populations of Hamatocaulis vernicosus is directly related with the state of their habitats. In undamaged mires populations of this moss species are abundant, whereas in drained fens and mires populations are small and in poor condition. It is necessary to prepare conservation plan for this species. The evaluation of natural factors threatening protected species populations revealed that the most significant are processes of succession in the communities and habitats. Many of these processes are underpinned by past human activities, in particular – drainage of wetlands. Populations and habitats of some species are highly threatened by invasive plant species. Wetland plant species are threatened by beaver activity. It was found that a number of species populations characteristic to open habitats are adversely affected by the severance of anthropogenic and economic activity (grassland and wetland habitat use), but the greatest threat to individual populations poses forestry and hunting activities: a lot of valuable areas with rare species habitats are planted by forest cultures. Recommendations for conservation measures of each investigated species and its habitats are provided. In the nearest future conservation plans for Agrimonia pilosa, Botrychium simplex, Dianthus arenarius subsp. arenarius, Linaria loeselii, Liparis loeselii, Najas flexilis, Thesium ebracteatum and Hamatocaulis vernicosus should be prepared and on the basis of conservation plans nature management plans should be corrected or action plans should be prepared and implemented.