Active measureas are taken for threatened species and habitats to improve their status. 

Main measures: 
1) Core legal framework for strict species protection (in situ).
Nature Conservation Act establishes protected species categories (I–III) and the legal basis for prohibitions, permits, and enforcement. The Act hardwires a habitat-based approach to reduce extinction risk:
o    Category I: protection of all known habitats via protected areas / limited-conservation areas or species protection sites;
o    Category II: at least 50% of known habitats (entered in the nature information system) must be protected;
o    Category III: at least 10% of known habitats must be protected. 
The Act is also explicitly used to implement the EU Habitats and Birds Directives, which are central for threatened species/habitat conservation in Estonia.

2) National planning instruments: species/habitat action plans.
Species conservation & management action plans are mandatory for Category I species and also triggered when existing measures are insufficient or required by international obligations. These plans define objectives, threats, priority measures, schedules, and budgets. 
Habitat action plans are drawn up when needed to ensure favourable condition of habitats (including where earlier measures are insufficient). 
Species protection sites (incl. nesting sites and seasonal movement restrictions) function as targeted “micro-protection” instruments for high-sensitivity species (e.g., certain raptors, black stork, flying squirrel).  

3) Monitoring, inventories, and evidence-based prioritisation (threatened species + genetics).
EELIS (Estonian Nature Information System) is the national database used to manage information on protected areas, nature values, and legal restrictions—supporting planning, permitting, and reporting. 
Monitoring data and reporting are supported by national monitoring systems (incl. Environmental Agency / monitoring information systems) to enable trend detection and adaptive management.

4) Regulation of direct pressures: exploitation, incidental mortality, and permitting.
Hunting is regulated as a sustainability tool, including governance mechanisms that make proposals for management of brown bear, wolf, and lynx and set/agree quotas for key game species. 
For fisheries, Estonia applies control programs and governance structures for sustainable management and protection of fishery resources and habitats (relevant for threatened migratory fish and spawning grounds).

5) Human–wildlife conflict prevention, compensation, and coexistence governance
The Nature Conservation Act provides for:
o    permissibility of non-lethal property protection measures;
o    conditionality: if preventive measures are not used, there may be no right to compensation;
o    partial compensation for damage (and some prevention costs) caused by specified conflict-prone protected species (incl. wolf, bear, lynx, European mink, etc.). 
Estonia complements this with species-specific coexistence frameworks, e.g. the Large Carnivore Action Plan 2022–2031, emphasizing systematic monitoring, regulated management, damage prevention, and also genetic considerations (e.g., population coherence / hybridization risks).

6) Invasive alien species prevention and management (to reduce extinction drivers).
Estonia prohibits releasing alien species into the wild and planting/sowing alien plants in the wild under the Nature Conservation Act framework and organizes permitting and management planning. This is aligned with EU Regulation 1143/2014 on invasive alien species (a key policy driver for coordinated prevention/management).

7) Genetic diversity conservation (wild + domesticated), including ex situ measures
Plant genetic resources (ex situ + use): Estonia maintains an ex situ gene bank (long-term seed preservation, collection from natural habitats and home gardens, access for users). The national Plant Genetic Resources programme 2021–2027 explicitly supports collection, conservation, characterisation and use of plant genetic resources, including stronger attention to crop wild relatives—directly relevant to maintaining adaptive potential. 
Domestic animal genetic resources (in situ + support instruments): conservation of indigenous / endangered local breeds is addressed through dedicated action/development planning and breeding programmes + state benefits. 
Threatened wild species (ex situ ↔ in situ integration): Estonia has internationally notable captive breeding + reintroduction capacity, e.g. Tallinn Zoo’s European mink work: ~600 individuals released on Hiiumaa (2000–2016), after removal/control of invasive American mink pressures—directly supporting recovery and reducing extinction risk.