Production of coral reef habitat maps from high spatial resolution multispectral imagery is common practice and benefits from standardized accuracy assessment methods and many informative studies on the merits of different processing algorithms. However, few studies consider the full production workflow, including factors such as operator influence, visual interpretation and a-priori knowledge. An end-user might justifiably ask: Given the same imagery and field data, how consistent would two independent production efforts be? This paper is a post-study analysis of a project in which two teams of researchers independently produced maps of six coral reef systems of the archipelago of the Primeiras and Segundas Environmental Protected Area (PSEPA), Mozambique. Both teams used the same imagery and field data, but applied different approaches—pixel based vs. object based image analysis—and used independently developed classification schemes. The results offer a unique perspective on the map production process. Both efforts resulted in similar merged classes accuracies, averaging at 63% and 64%, but the maps were distinct in terms of scale of spatial patterns, classification disparities, and in other aspects where the mapping process is reliant on visual interpretation. Despite the difficulty in aligning the classification schemes clear patterns of correspondence and discrepancy were identified. The maps were consistent with respect to geomorphological level mapping (17 out of 30 paired comparisons at more than 75% agreement), and also agreed in the extent of coral containing areas within a difference of 16% across the archipelago. However, more detailed benthic habitat level classes were inconsistent. Mapping of deep benthic cover was the most subjective result and dependent on operator visual interpretation, yet this was one of the results of highest interest for the PSEPA management since it revealed a continuity of benthos between the islands and the impression of a proto-barrier reef.