Using machine learning algorithms to decode intended behavior from neural activity serves a dual purpose. First, these tools can be used to allow patients to interact with their environment through a Brain-Machine Interface (BMI). Second, analysis of the characteristics of such methods can reveal the significance of various features of neural activity, stimuli and responses to the encoding-decoding task. In this study we adapted, implemented and tested a machine learning method, called Kernel Auto-Regressive Moving Average (KARMA), for the task of inferring movements from neural activity in primary motor cortex. Our version of this algorithm is used in an on-line learning setting and is updated when feedback from the last inferred sequence become available. We first used it to track real hand movements executed by a monkey in a standard 3D motor control task. We then applied it in a closed-loop BMI setting to infer intended movement, while arms were restrained, allowing a monkey to perform the task using the BMI alone. KARMA is a recurrent method that learns a nonlinear model of output dynamics. It uses similarity functions (termed kernels) to compare between inputs. These kernels can be structured to incorporate domain knowledge into the method. We compare KARMA to various state-of-the-art methods by evaluating tracking performance and present results from the KARMA based BMI experiments.