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Background: In most trypanosomes, endo and exocytosis only occur at a unique organelle called the flagellar pocket (FP) and the flagellum exits the cell via the FP. Investigations of essential cytoskeleton-associated structures located at this site have revealed a number of essential proteins. The protein <i>Tb</i>BILBO1 is located at the neck of the FP in a structure called the flagellar pocket collar (FPC) and is essential for biogenesis of the FPC and parasite survival. <i>Tb</i>MORN1 is a protein that is present on a closely linked structure called the hook complex (HC) and is located anterior to and overlapping the collar. <i>Tb</i>MORN1 is essential in the bloodstream form of <i>T. brucei.</i> We now describe the location and function of BHALIN, an essential, new FPC-HC protein. Methodology/Principal Findings: Here, we show that a newly characterised protein, BHALIN (<span style="text-decoration: underline;">B</span>ILBO1 <span style="text-decoration: underline;">H</span>ook <span style="text-decoration: underline;">A</span>ssociated <span style="text-decoration: underline;">LIN</span>ker protein), is localised to both the FPC and HC and has a <i>Tb</i>BILBO1 binding domain, which was confirmed in vitro. Knockdown of <i>BHALIN</i> by RNAi in the bloodstream form parasites led to cell death, indicating an essential role in cell viability. Conclusions/Significance: Our results demonstrate the essential role of a newly characterised hook complex protein, BHALIN, that influences flagellar pocket organisation and function in bloodstream form <i>T. brucei</i> parasites.