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 eigendecomposition 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.