More than 205,000 records of botanical data were digitized into the Tropicos database (http://tropicos.org/) of Missouri Botanical Garden from Antananarivo, Paris and St. Louis. From those collections from Madagascar, several analyses were conducted to provide information to support decision making within the activities of Research and Conservation at MBG Madagascar Program. An objective of this research is to use Biodiversity Informatics to identify potential new areas for future botanical explorations. To do this, we developed a geographic information system including all geo-referenced botanical data collections of Madagascar extracted from the Tropicos database. We then used ArcGIS to establish standard observation grid cells to estimate the distribution of the number of collections in the Island. The values ​​of botanical collection density are calculated and presented according to several scenarios based both on the forest cover percentage estimated in the observation grid cells and the number of corresponding collections. The results obtained allowed us to present trends in botanical collections for several decades and in various areas according to their level of botanical exploration. These results were also presented with the new network of Protected Areas in Madagascar to deliver a tool for decision making for sustaining biodiversity.