In the selection of reserve networks there are special sites whose ecologic, strategic or morphologic values dictate their inclusion. The existence of regional rare or confined-distribution species is one among other reasons that often determines the existence of such mandatory sites. Moreover, quite often these mandatory sites are located far apart. Although several methods have been proposed to accommodate structural connectivity in reserve selection, they were not devised to deal specifically with such mandatory sites. Those that encourage aggregation of sites by means of criteria incorporated in the objective function do not seem suitable to acquire consistent connectivity levels in the presence of mandatory sites. Methods that enforce “full connectivity” tend to produce long and narrow solutions, which results in efficiency deficits and biological unsuitability, as they force the selection of more sites of less quality to ensure connectivity. Hence specific methods to select ecological reserves when mandatory sites exist are needed. Here we discuss and propose a 0–1 linear programming model to deal with this issue. The model was applied in two data sets of forest breeding birds and butterflies. Its solutions and computational performances are discussed.