Mangrove forests of Mexico have been threatened by the effects of anthropogenic activities during the last decades, mostly related to aquaculture, agriculture, livestock and urban development. Genetic diversity and fine-scale genetic structure of two generations of the black mangrove Avicennia germinans (L.) Stearn were investigated in perturbed and preserved sites from three lagoon systems in Sinaloa, Mexico. Genetic diversity and overall genetic structure were similar between perturbed and preserved sites. However, lower levels of fine-scale spatial genetic structure were observed in two of the younger (sapling) generations. We attribute this to differences in local dynamics of each lagoon system, their status of conservation and levels of fragmentation. Also, low connectivity and the effects of disturbance could restrict the movement of pollinators and seed dispersal capabilities, resulting in low levels of genetic diversity and signs of inbreeding. Perturbed populations of A. germinans may play an important role in in situ conservation of this complex ecosystem.