Urban development is driving the loss and subsequent fragmentation of mangrove forests in Penang, Malaysia. However, little research has focused on the implications of urbanization onto the biodiversity within mangrove forests. This study investigates and compares both vegetation and crab assemblages between urban and rural mangrove forests. Collectively, 5853 trees were recorded including 15 species from six families: Acanthaceae, Arecaceae, Lythraceae, Malvaceae, Meliaceae, and Rhizophoraceae. Avicennia marina accounted for 88.6% of all trees in the study and held the highest species importance (IV). Although the total number of mangrove tree species varied significantly between urban (14) and rural (7) mangrove forests, the mangrove forest structure based on IV did not vary significantly. In total, 633 crabs were recorded comprising 13 different species from three superfamilies: Grapsoidea, Ocypodoidea, and Paguroidea. Crab species richness did not vary between urban and rural sites, but the biomasses of five and the densities of four crab species varied significantly. Redundancy analysis (RDA) indicated that land use, salinity, and abundance of Avicennia officinalis can best describe the distribution of crab species (r2 =32.7). This study indicates that smaller fragmented urban mangroves at the east coast of Penang have a relatively high tree and crab diversity and are worth protecting, in addition to the larger mangrove forests on the west coast. The preservation of small yet interconnected mangrove sites could be critical to the recruitment of their flora and fauna and should be considered in decision-making processes.