The Long-Term Monitoring at the East and West Flower Garden Banks National Marine Sanctuary 2002-2006 data include biological and oceanographic measurements collected to satisfy the MMS and NOAA contracts 1435-01-02-CT-85088 and 1435-01-04-CT-33137 through the monitoring year 2006. The Flower Garden Banks are located in the northwest Gulf of Mexico and are unique within the region. The Flower Garden Banks are coral reefs with biological assemblages typical of Caribbean coral reefs, including approximately 23 Caribbean scleractinian coral species, a low abundance and diversity of sponges, and reef fishes. These data are the result of yearly monitoring events and are used for comparison purposes required to complete technical reports and presentations. Statistical analyses, photographs, and videography are not included in this submission. On the East and West Flower Garden Banks there are 100 m by 100m study sites within which monitoring is conducted every year. The data included in this submission are from these study sites and include the following: (1) random transect benthic cover data obtained using videography (2002-2006), still photographs (2002-2003) and linear point intercept observer data (2002-2003). Random transect data include the proportional cover of benthic components including coral species, sponges, algae, and other groups. (2) Sclerochronology data are taken during odd years to look at short-term (10 years) change in coral growth rates. (3) Photographs of marked Diploria strigosa colony margins are taken annually to track lateral growth or recession of colony margins over time. Data within this dataset start with comparisons between 2001 and 2002. (4) Repetitive 8m2 quadrat planimetry data follow specific coral colonies over time. Coral colonies are traced each year to measure lateral growth, loss, and/or replacement within a continuously monitored 8m2 area. Data within this dataset start with comparisons between 2001 and 2002. (5) Abiotic water quality parameters are recorded on a continual basis using YSI datasondes. Data include temperature, specific conductivity, dissolved oxygen concentration, dissolved oxygen charge, pressure, depth, pH, pHmV, par1, par2, turbidity, and salinity. Additionally, HoboTemp thermographs are used as a back-up to record temperature. On YSI datasonde changeout cruises water samples are taken at surface, mid-water and at the benthos for nutrient and cholorphyll analysis. (6) Fish population surveys are completed to monitor fish species abundance and size from year to year.