This paper presents a research software solution specifically developed to allow marine scientists to produce geo-referenced visual maps of the seafloor, known as mosaics, from a set of underwater images and navigation data. LAPMv2 is a suite of tools, which provides the users with the current state-of-the-art methods for automatic feature detection and matching, as well as with powerful tools for registering images, constructing and geo-referencing photomosaics, and importing them into geographic information systems such as ArcGIS. The main key strengths of LAPMv2 include (1) its robust false-match rejection method, which allows the application to run fully autonomously without producing aberrant results caused by erroneous matches, (2) the total control of the user over the mosaicking workflow, (3) the possibility to intuitively create matches between unlinked images, and (4) the graphical interface that guides the user through the different steps of the mosaicking workflow.