Since 2002 two areas in southern Louisiana (Caernarvon Breton Sound estuary and Atchafalaya basin region) were studied regarding the occurrence of the invasive and potentially harmful cyanobactenum Cylindrospermopsis raciborskii. In the Caernarvon Breton Sound estuary, the species was detected for the first time in Louisiana in July 2002 in Grand take during monthly phytoplankton monitoring surveys. The species occurred again in the estuary in summer and fall 2003 and 2004. Three distinct morphotypes (straight, curved, curled) were present, with the curved or curled varieties usually most abundant (> 80%). During summer 2003 the cell numbers in Grand Lake exceeded the critical level of potential toxicity (> 20 ×106 cells liter-1). In 2004 the species was a rare sight in the estuary and was not detected any more in 2005. In the Atchafalaya basin region, C. raciborskii was frequently detected in fall 2004. The greater Lake Fausse Pointe area was especially a hot spot, with critical level abundances up to 30 × 106 cells liter-1. In both areas C. raciborskii occurred only in summer and fall at elevated water temperatures (> 25-33 C). It was more frequently detected in the southern, less diversion-influenced part of the Caernarvon Breton Sound estuary, whereas it occurred more often in the northern part of the Atchafalaya basin. The species was present in a conductivity range from μS cm-1 700 to 10,000 within the Caenarvon Breton Sound estuary. Samples containing Cylindrospermopsis generally were significantly higher in total and cyanobacterial chlorophyll compared to samples without Cylindrospermopsis. © 2007 by the Marine Environmental Sciences Consortium of Alabama.