Arid mangroves constitute a particular biotope, with very extreme variations in ecological conditions, mainly temperature and salinity, condition that demand specific adaptations to successfully inhabit this ecosystem. Cyanoprokaryotes have not been well studied in Mexican coasts and this is the first study that contributes to the knowledge of the biodiversity of this group in an arid mangrove in Zacatecas estuary, Baja California Sur, Mexico. Samples of Avicennia germinans pneumatophores from Zacatecas estuary were collected between May 2005 and May 2006. The identification of the most representative Chroococcales produced 10 morphotypes, described morphologically and digitally registered for the first time for Mexico. We report species of Aphanocapsa, Chroococcus, Hydrococcus, Chamaecalyx, Dermocarpella and Xenococcus. Some taxa have been recorded in brackish or even marine environments from other regions, evidencing the wide geographical distribution and ecological adaptability of these organisms, but some others are probably new to science. Some species have a specific seasonal and vertical distribution on the pneumatophore but other have a more ample distribution. Aphanocapsa littoralis and Chroococcus cf. obliteratus are new records for benthic biotopes of Pacific Mexico; Dermocarpella cf. stellata is a new record for the Gulf of California.