The isometric mapping (Isomap) algorithm is often used for analysing hyperspectral images. Isomap allows to reduce such hyperspectral images from a high-dimensional space into a lower-dimensional space, keeping the critical original information. To achieve such objective, Isomap uses the state-of-the-art MultiDimensional Scaling method (MDS) for dimensionality reduction. In this work, we propose to use Isomap with SMACOF, since SMACOF is the most accurate MDS method. A deep comparison, in terms of accuracy, between Isomap based on an eigen-decomposition process and Isomap based on SMACOF has been carried out using three benchmark hyperspectral images. Moreover, for the hyperspectral image classification, three classifiers (support vector machine, k-nearest neighbour, and Random Forest) have been used to compare both Isomap approaches. The experimental investigation has shown that better classification accuracy is obtained by Isomap with SMACOF.